I have been playing through the Early Access and am enjoying myself. The game is obviously incomplete, but as many have suggested on the forums that several ES2's systems and designs currently do not work as stated or intended in the game design documents. One of the best summaries can be found by XDAvenger93 and his post here:

https://www.games2gether.com/endless-space-2/forum/66-game-design/thread/21526-the-curios-case-of-the-game-that-played-itself?page=1#thread

Sotnik has a new thread that has some ideas, but it is a complete bottom to top rework, which has some good ideas, but I do not think is feasible. It can be found here:

https://www.games2gether.com/endless-space-2/forum/66-game-design/thread/21737-making-the-game-be-played-by-yourself-tech-table-suggestion-and-a-bit-more

So to break down XDAvenger93's main point, is that the tech tree offers few choices. You are railroaded into mandatory techs just to unlock basic game features, and then if you ever try and go back and pick up some non mandatory techs, it punishes you by science inflation. This makes for optimal tech paths for each race with little to no deviation. 

I have what I believe is a novel solution that allows the player to experiment with their tech choices, respond to changes in the game state, and make some progress along all of the 4X's without completely hamstringing as well as making the Eras feel more meaningful and significant. There are several mechanics mentioned in the GDD documents that talk about linked techs and discounts between techs, but those are not implemented yet and I am making suggestions based on what is in the game.

The Idea

The basic mechanic change I am proposing, is that at the end of each Era, when you progress to the new one, to learn all the previous techs from the past Era. This idea is completely unbalanced without combining it with several other mechanics. First, each tech you research would have an end of Era bonus. Each tech you did not research would have an end of Era penalty. The easiest way to do this would be industry costs, but could possibly have upkeep changes as well. 

Example:  Say you unlock 5 out of the six Era1 Science techs, you would then get a 15-20% industry cost reduction on building any science related improvements and on support modules in Era2, and on your new colonies that are not up to date. Conversely, if you got none of the military technologies, you would get a 10-15% penalty to all military improvements and modules, including upgrade costs. This means thematically, once you reach Era2, you can build military based ships with Era1 military tech, but they would be at an increased industry cost and possible increased cost in strategic resources or upkeep. This would also mean that new colonies of yours could easily produce science buildings, but that military or other buildings would be neutral or extremely expensive, which would fit the theme of the empire you are building and what you are good at.

I want to quickly put in one other non-Tech Tree related enhancement I would add to this idea. Improvements or Ships built with the previous Era's technologies WOULD NOT effect the political leanings of your populace. This makes sense thematically. No one is really impressed by the last Era's technology. To bring in a real world example most people are not impressed with the idea of a new train in their country, even a high speed one or mono-rail, but the HyperLoop idea is something a lot of people get excited about. 

This means that after Era1, you could continue expanding and pushing your science while building just enough fleets to defend yourself, without the Militarists taking over your senate, or you could quickly research Era2 Military techs and build fleets and go on the warpath. The idea that each new Era you have the previous efforts of your civilization to build off of, but that at each new Era you could forge a slightly new path whether by choice or by the state of the game. 

This would also help the Devs balance the game as they would know that by Era2 everyone would have access to certain resources and gameplay elements, just at differing efficiencies. This means possibly making system improvements require strategic resources like in ES1, which I was shocked to find was not in ES2, but I could understand once I saw how the resources were gated with the exponential science costs.

With this change it means that if you do not put any research into one aspect of the game you still are technologically only one Era behind, and it might cost you more to build those improvements or ships, but you could still at least still participate in this aspect of the game without a such a punishing penalty. This would keep the science inflation mechanic that gives a player the ability to just choose which order they want to research each Era, but they would at least get the techs from previous ones. 

Problems with the Idea

The biggest problem with this idea is that it makes the Sophons and their focus on science much too powerful, as well as the Oracle of Science law completely broken. Other problems are layered by Era. If you focus on Science and Expanding Era1, then the Military Era2, will you still have penalties from Era1 not focusing on the military into Era3 even though it was your focus in 2. Will the bonuses from Science in Era1 trail over into Era3 science techs? Or were they only for Era2 techs? Or will it all be cumulative? I could see a game were you focus on Science and every era you focus on it, and the bonuses get so large and that is what propels you to the science victory. Or for the military over five Eras your ship and improvement costs get so cheap that you can just flood your opponents if you want to win that way. 

Conclusion

There are a lot of problems, potential problems, and balance issues with this approach, but it solves three major pain points (or tries to). First; with so many mandatory techs you only have one tech path per race, but now if you decide to go a slightly different path you know it does not lock out other Victory Conditions. Second; focusing on one or two paths or Victory conditions does not mean you have to completely abandon the other ones. Finally, trying to complete some aspects of all 4X's completely destroys your senate. While this approach may not work, I believe it is an idea worth discussing further. 

I'm not saying it's a bad idea. But I don't see the point as it seems to overcomplicate the balance, where they could design a tech tree closer than what it was in ES1 and it would work very well.

The adventage of a classic tech tree is in the name of the thing : it's a tree. It means that you start out with a few things that allow you to discover more and more numerous and complicated things. And this picture suit very well with the dawn of a civilization that will expand, which sums up what Endless Space story is. The actual system isn't good for this, nor imho your idea is.

The problem with your idea is that you still have this limiting factor that doesn't suit this civilization growth idea. With your idea we still have the weird impression that we manage to achieve great science prowess while still being stuck with basic stuff. What you say sounds like you automatically half-research what's in last era, so you still can build it but if you want to build it for cheaper you can do the research. It doesn't sound right to me. Mostly because you don't have a half a technology. Let's say you want a fusion reactor. You know how to build it, or you don't. There's no half way. If you spend more time studying fusion reactors you'll maybe improve it make it more powerful etc. but you'll surely not need less bricks to build it. Furthermore I see a balance issue. You'd just need to blast trough industry tech tree, discovering everything else at the same time, and building it without caring about the penalty.

These are issues that aren't existing with a classical tech tree.

If they want to keep this system up, I think the best call is to give strong science bonus to research last era tech, but it's not as good as what they've already done in ES1 so I really don't see why they bother with this era system.

Here what i posted elsewhere but it also applies here. (Even more)

Right now ES suffer from a great problem that is called Lack of 3D perspective.

As in many space games out there, including ES1 we do not have a galaxy.

We have a monopoly board with colors and picture of space.

This could be manageable... IF the developpers clearly were thinking 3D, but unfortunatly they haren't. The dev aren t in space, they are still on Auriga...-> Flatland ->2D mentality. Not 3D mentality as a space game would require.

 This plainly show up on the universe, obviously 2d, on the combat with its total 2D mentality.

Lets get some reasoning. I have a ship with rotating guns above my "wings", and the body of my ship block a certain amount of degrees and latitudes of my firing possibilities. Now lets consider the left and right guns + the ones on the "dorsal" of the ship that can swivel anywhere on a half sphere. 

If i am attacked and am defending my life why would i not totate the dorsal of the ship toward the ennemy fleet and present all my weapons to them why woud i loose an entire section of weaponry staying exactly like 2 cars at each other side ?

It is also noticeable by the fact there no "ventral" weaponry leaving the ship as a fish or dragon...weak skin on the belly.

But there s no risk there because ennemy can only attack me by one side , left or right, not up not down not front not rear... and they will quite remarkably level to me during all combat, nice doggy. Multiple angle attack ? hah!! impossible...Noone is that smart.

This locked 2D mindset also show up in the tech tree, flattened mind on full display.

Instead of thinking "what can we do and what haven t been done before and would be cool"  Its OMG we don t know what to do lets copy what has been done.

What i liked in ES1 tech tree was the fact that there seemed to have a logic in techs order in the tech tree. It wasn t inovative but it was diferent from EL (i layed EL first and ES after but i know the release order is otherwise). 

My suggestions would be: Strenghten the cause-consequence of the techs but instead of making 4 totally separated tech, try to link some tech from branch A to branch B, C or D and so on.  

Instead of spreading out totally separated branches you could have a cone shaped tech tree that you would rotate (3D artist needed here) and when viewed from above you would have ramification crossing the inside space of the funnel shape.

Not sure i was great trying to build a mind picture on you people, so i will join a bad drawing to a bad explanation...

Black, Red, blue an green are the kind of tech (afaik number of diferent techs could be 4, 3, 6, 2 whatever)

Those are linked the way they were in ES1 indicating reshearch possibilities.

But as they are not spread out in a 2d space but rise as a glass of.... wine, whisky, vodka, beer (choose your kind), they can be linked togheter in 3d space...

As an example a blue tech can be necessary to acquire some red tech, or could be another way to reach it. So black (who should be the nearest perspective in the drawing, can link to a blue one (fartest) as well as a green could link to a red, blue or black one.

Second point:It could be interesting to create, as option, a surprise factor and so booster replayability. Lets have a randomize skill tree option.

Example:

On the vanilla tree, lets say that to acquire AP (armor piercing) Missiles , a red tech,  you need to know how to colonize (blue tech) or industrially explore**** (this is another subject - Why the hell have we to colonize an entire planet to acess its ressources, even parcially? Does all diamond or gold mine have a full fledged city near it ? Or just the kind of infrastructure that is needed for the workers? Can we have Exploitation split from colonization? At least for some case like Icy/thundra/boreal whatever Planets. Sorry long rant) ****kind X planets to be able to collect Material Z that only exist in these kind of planets and, let say, you would also need the knowledge on propellants (black tech) to create enought speed  to be able to pierce ennemy armors.

Now, on second run, as you now, know the tech tree by heart, you decide to increase the emotion calling some "discover" factor.

You press a button called "randomize tech tree" and now to build the same missile, you don t need Icy planet but lava planet, and doesn t need a specific propellant anymore.

This way we have many effects on the game:

Basic:

1) The techs requirements are scrambled (at least part of them)

Advanced:

2) Tech requirements can expand or shrink in numbers of pre-requisites to be reached

3) Some tech will exist on some random trees and not on others.

And i would add another optional feature: The mystery tech tree.

Basic:

You don t see the whole tree, only the techs avaliable to you with what you have discovered, but you see, the kind of tech (color) and what you will find (the tech per se)

Advanced (and quite masochist):

You don t know for sure what you will find but you know the kind of application it can lead - You only see the tech color not the exact result it will produce.

Disclaimer:

1) If you missed the word "optional" somewhere add it at will.

2) Critics mode on i m here to take flaks, those are just ideas to play with.

3) I m obviously aware that this lead to a rethinking of the tech tree concept and can take time and be frustrating at the end. BUTT, AFAIK, and i can be very wrong, if people ever thought as far, nobody never displayed it in a game. AFAIK i m pushing some boundaries there, and there can be some tech constraint(but i highly doubt it, this is almost as simple as a pool of questions to simulate an exam), what is needed here is an individual techonology examination to see what can be randomised and how deeply, what remains interesting and what is too static. Design thinkers, double diamond is prossibly necessary here. (those who knows, knows) 

4) Doesn t need to be 100% random, just what is plausible, but as an example: why the hell Icy planets are always for any kind of civilization harder to be colonized than thundra ones...or than boreal with high radiations level. Why the hell Material X is always harder for any kind of civilization to extract and be used and always result in more damage agaisnt any kind of tech than tech Y. 

Fueur Fir!!!