For starters, I would like to post this thread here:
https://www.games2gether.com/endless-space-2/forum/66-game-design/thread/21749-fixing-tech-tree-ideas-discussion
Which poses some great grounds on what I am about to analyse bellow. 

For starters, I do agree with most, if not all of the comments regarding the Tech Tree. Although personally I like both the ES1 and EL tech system, ES1 provides with variety, flexibility and a greater idea of what your empire's playstyle is going to have, while EL tech offers a more linear path, true, but more focused on action packed fast games. 

Personally I think ES2 has a chance to have a combination of both, more on that bellow. I feel however that so far, the greatest wasted potential of this game (yet) and the reason why I would not reccomend it to someone while a gem such as ES1 is out there, is the political system. Let me explain and build upon the thread and reccomendations posted in the thread above.

I think the idea of splitting the technologies so we have more available to us and more variety is a good idea. I also like te idea of having the ability to beeline towards a specific tech (ex, tier 5 ships) while ignoring the rest (something which was easilly available in ES1). That said however, I think just spliting them would be a wasted opportunity. Lets face it, the game at hand is one among a sea of very strong (and more to come) space 3X games and so far it does not offer much to draw attention aside from the amazing story, art and well, series it is tied in. Except from one thing, the motto. 

"Your Vision, Their Future/ Their Vision, Your Future" is something that, tied with the political aspect at hand, is something that has intrigued me since it offers a more volatile and realistic political gameplay in addition to those sweet sweet space battles, and so far I am dissapointed to say that I have not seen them come into play in any way, aside from just outlining my gamestyle. 

The problem I have had so far while playing space inquisitors (Vodyani) is that, for starters, I have no idea how to increase the religious party's influence, since siphon essence, I needed strong ships to defend the siphoning ships, not to mention, with Cravers breathing down my neck, I needed more fleets to guard my few systems and hold on to the systems i was intending to colonise, so as you understand, I had to spam powerfull ships to manage, which resulted in the Militarists having rave parties in my congress, with no outcome at all, since I basically just picked the same decrees I wanted, but with a "militarist" name slapped in front of em. This, I think is a wasted opportunity and I think that it can be expanded to make things complicated, I would not even mind if we had rebelions. We are a sci fi game, lets add more aspects of sabotage, rebelion and intrigue!

Now that the intro is done, lets go with the suggestions

Have the poligical factions have distinct influencial points of your empire

Militarists: Ships, Land Battles, Conquest, Military expansion etc

Diplomats: System Defence, Alliances, Diplomatic Actions (compliments, insults etc), Peace Treaties

Scientists: Science Buildings, Tech Tree acquisition

Religious: Buildings and Tech that increases population Happiness (Religion has been a way to control morale in masses for eons and has been instrumental to the public's happiness, either providing hope or supplies)

Ecologists: Food Production, eco-friendly choices

Merchants (Economists?): Dust production, trade agreements etc

How this will come into play I will explain bellow. 

A) Split the research tech trees into faction related trees. You start with being able to research all tier 1 technologies from all factions, however

Progressing through the tech tree goes exclusive to each faction and increases their influence. For example, this way you can beeline to your tier 5 ship, knowing it will give the Militarists a huge boost, that would affect the choices greatly since:

B) Military Parties give bonuses but also lead to friction with their "opposing" faction. So for example, in the previous example, you would have a strong military pressence and the planets that are pro-militarist will be happy, but that would lead planets that have their rivals (diplomats for example) would lead to less happiness, to downright strikes. So for example, neglecting one party too much, may lead to unpleasant surprises. From Strikes, to downright splinter factions to "rebelious" systems etc. 

C) Faction relations can lead to more options for decrees. For example two non-opposing factions can unlock themed decrees, for example, high militarists and high religious parties can lead to having a combined decree of "royal inquisition" for example, which would suppress the other factions. I think this can allow the players to either go for a full blown dictatorship, or a more democratic middle ground, trying to hold a balance between the factions

D) Choosing who  you support may influence things, for example if you have a Military superiority both in influence and in systems that represent their interests, maybe if you choose their opponent faction, or not support them enough may lead to them trying to overthrow you, the means to which can depend upon factions. Ex

Military: Rebelion

Diplomatic: Assassination
Religious: Civil Unrest to a crippling ammount etc

I think the above would be an interesting addition and add the game's moto in a gameplay mechanic, since you will have to adjust your policies depending on what your people want, while the overall political current is in the same time influenced by you. 

Another thing I would like to put some suggestion to is the land battles. 

I love how they look, and the aesthetic of it, however I feel like its lacking, and its here mostly for flavor than an actual system. How about you add 4 types of land units, 3 types of armor and 2 types of aircraft for land battles and the players get to pick the composition of them? They can be thematic too, for example, in EL, Vaulters had marines, chargers and the golems, so similarly you could have a theorised Vaulters faction in ES2 have Marines (good in infiltration), Chargers (good in blitz) and the golems to be better at the pre assault bombing phase. Similarly with armor and aircraft. I think this will give more variety to the players and get them to have more than just flat stats to decide how they will proceed, but actually have to base their decission based on their unit composition.

Another idea that ties in with the suggestion above, is to have one standard unit, and then depending on which faction you bring to a specific tier, you unlock an additional thematic unit for that faction, which makes the population a bit more predesposed to that specific mindset. For example, you use a full Religious army to conquer a planet, have the religious faction get a small bonus on the influence of that planet etc.

What do the rest of you think? Overall despite it all I enjoy the new style, menus and the smoothness of which it runs. I admit I kind of liked the customization on the ships of ES1 and the modules that increased how many things you could put in your ship there, but the customization in ES2 is ok as well

The tech tree update has already been decided upon, so just as a precursor, none of this discussion will matter. That said:

Allowing players to make a beeline for certain technologies runs in direct opposition to the Era system. If there's a method of ignoring certain techs to rush later ones, you have a tech tree where the branches are invisible. If remove all dependencies to allow rushing of later technologies regardless of most prior technologies, you have a tech blob, more akin to Age of Wonders III.

Unfortunately the straight Era system has to be fairly linear, that's the unfortunate reality of the system. Which I will concede, is probably helpful for those hoping to learn 4X gaming.

Thats true, never thought of it that way, though, I think have more faction oriented tech trees would also help ,since it would make political parties both affect your gameplay and make it easier for you to understand whats up. The way the system is right now, the political factions do pretty much nothing to affect your gameplay