I just want to piggy-back on this excellent post by applecat.  I agree with him absolutely that Science throttling is very stiff in the game, which has a variety of knock-on consequences, the worst of which is that it can be difficult to adjust your strategy to new developments.  I have only gone on two playthroughs, each to around turn 60 at which point I felt as though I had dug my civ into a bit of a coffin (for different reasons).  These are just general balance thoughts.

CRAVERS

• What a rush to play!  I went what I felt to be the obvious route, building a basic infrastructure then cranking out Slicers and settling/invading rapidly.  As often happens once you hit your stride in the early-game with these sorts of "Zerg Rush" factions, I had 4 or 5 systems many of which I took within the space of a few turns of each other.  One was from rushing a Colony race against the Lumeris, one was from invading a system with even more Kalgeros (huge mistake), and the others were from my own colonies.  The first thing that happened as this played out was my Happiness tanked, as every election was giving me absurd maluses from the minor/major faction pops I ended up.  By the time I realized the problem I was out all manner of FIDSI on all worlds and my population levels were sinking at a delirious rate (the Kalgeros I began with were hilariously evacuating my core worlds, which at least felt almost like a self-fixer).  Looking back at this, I mostly only have myself to blame, it's necessary to have these sorts of checks against wide aggro strats.  However the Happiness problem was relevant from the very first election, where my native Kalgeros pop gave me a 15 or so percent Happiness malus to my civ (as a side effect of Totalitarian gov't).  This was a harbinger of the pain to come.

• I dug myself out of that problem with hero reassignments (Loyal Flock is a vital faction trait I guess!) and a hasty research grab at Infinite Markets (around turn 30 or so) and was running my quest line finally, having settled down on the new colonies for a good bit.  I had chosen the Religious branch of the Craver quest line (I'll be vague to avoid spoilers).  A couple of links into that chain I obtained an item which needed to have a custom quest structure built on one of my planets for it.  This structure's costs included 50 Titanium and 50 Hyperium!  I was alarmed and dismayed, as due to the nature of my early expansion rush I had grabbed both strategic resource weapon/defense techs and gone on an upgrade binge with my ships, which was critical to letting me succeed militarily.  I had lucked into some replenishing Titanium resources (around 2 a turn...) but there was no Hyperium on planets anywhere near me, so I was trapped in this quest line.  I think this is a symptom of the current nature of the Loot/Resource system, which seems to favor giving players strategic boosts of Loot, but is much stingier about providing systems with a renewable Strategic resource to exploit.  I think that's nifty and a nice take on the concept, but I am concerned that tying too many important structures to those same resources is inevitably going to result in problems for any civilization which wants to benefit from strategic-boosted fleets.

• It was at this point that Research throttling was starting to really clamp it's jaws down on me.  I was stuck on Tech 7 or 8 or so of Era 1 for almost a dozen turns, resulting in a turn 50-ish position of me sitting with most of my systems unable to build anything other than ships due to lack of new technologies, and all of my upgraded military ship designs were impossible to build because I had burned through all of the Strategic resource Loot that was fueling my war engine.  At this point I called it a game, having hit a sort of natural end point where the next dozen odd-turns would be me frantically righting the ship (again), this time with Science as the arbiter of my civilization going horribly off-course.

SOPHONS

• Unlike the previous game I found no nearby Major or Minor civs for a long while, so ended up focusing my early Research on Colonization boosts.  In no time I had plenty of planets to choose from, including another Veldt system for that sweet Science and a Jungle/Tundra combo planet system.  It seemed too good not to go for them!  This began yet another wide strat playthrough for me, which resulted in some very similar problems to my first.  Interestingly, I discovered very quickly that my home system (with Drone Network) couldn't sustain population well at all, in fact after getting a mere one extra population it reversed course dangerously close to population regression.  I used my first Hero as a governor and gave him both levels in the 'Neutral hero' line of Food/Manufacturing pop bonuses to keep my home system's population stabilized until I could research and build some agriculture improvements.  This was a big speed bump to getting my science improvements up, and by the time they were up I was a colony or two into the game and already finding Era 1 Technologies to be abnormally burdensome for the supposed 'science race', I assume due to the expansion penalty.  From this point on I had to struggle to get back 'on the curve' of the Science costs.

• Again, political factions became another minor disaster as an early-game Science Law I scraped up the influence to pass was abruptly struck down by the first big election.  Pacifists had taken nearly 60 percent of my senate, so I ended up running a split Pacifist/Scientist government at this point for the rest of the game, which was rather fun once I'd adjusted, especially once I started cranking out SPIN planetary improvements to generate a lot of influence so that I could work better with the whims of my political system  With the Pacifist mandatory law I was able to peacefully annex some Mavros which seemed like it would be a fun reunion for all involved.   Still, it felt very abrupt to lose any hope of the stronger Scientific laws (requiring Broad or greater support).  Maybe something could be more clear in terms of how you can manage to stay the course with your starting faction?

So, some quick final thoughts:

• Tier 1 Support Ships feels pretty sad :  I didn't actually touch on this above but it very much feels this way based on both Sophon and Craver fleets where I tried to make this ship do work for me.  The support modules at the start of the game simply don't do enough.  Including one of these Support vessels in your early-game military fleet (instead of an Attacker) is a massive compromise in that fleet's damage output, so the support modules need to be a lot stronger and feature more choice in powerful fleet-wide bonuses to be at all worth investing in IMO.  The extra defense modules it gets are nice but don't make up for this... maybe a cheap no-research-needed module that makes the Support ship more likely to get targeted by enemy attacks?  One other idea I had to introduce a bit of relevance to this ship class was, in Tier 2 technologies, swap around the "tier 1 ship upgrades" so that researching your Tier 2 "Hunter" hull gives you also an upgrade to your Support, while your Tier 2 Support vessel would give you the bonus slots to your Tier 1 Attacker.  This would seem to introduce a bit of diversity to fleet compositions between civs and playthroughs, and make that Era 2 tech choice more intriguing.
• Minor Faction pops on your home planet at start is weird and I don't think I like it :  This feels at odds with the nature of the rest of the game's design, where a fancy non-standard 4x game element is eased in on you over the course of the early stages of the game.  For both of my playthroughs above, it felt like I was already in damage control on my Political parties from the very first election.  I love the population and faction mechanics though!  They're great.  But with a minor faction pop that is just waiting to throw your first election into chaos,  it feels thrown into your face as a punishment at game start without any obvious recourse aside from 'gaming' that mechanic in very deliberate rehearsed ways.  I would be all for your native faction pops manifesting the first 'alternative' political faction outside their norm fairly quickly at game start so long as it's at least telegraphed, even that would probably go a long way to reducing that frustration.
• Maybe look at the Strategic Resource allocations a bit more closely? :  Due to Research gating your ability to settle new systems and based on how the balance between Loot vs. Exploitable Resources appears, it seems to me like it can randomly be pretty hard for a player to obtain Titanium or Hyperium based solely on the galaxy generation at start of game.
• Research throttling appears busted for real though:  This was a strong contributing factor to lethargic 'slow-downs' in both games I've run through thus far.  Even for the Sophons, I felt a lot of difficulty adjusting my strategies based on new information about opposing civs/the galaxy due to how 'heavy' the steering is here.  Every technology I chose to research after the first half dozen was a heavy decision, which could I guess be good in some ways but felt crippling.  With the way that major features of the game like Trade Companies, Luxury Improvements, Diplomacy, etc. are gated by Science (and well into Era 2 at that) it is very slow to actually get to use more than 1 or 2 of those features.  In fairness I need to try a Tall strat next to compare and contrast though.