Fixing the stuff with a mod is possible, but would be a massive undertaking, so hopefully someone is still in charge of the game over there able to get this game on track again.
Um... not particularly massive, I addressed the majority of this list for IAB weeks ago. For example:
-Starting abilities are a complete failure at the moment, and not balanced towards the current resource design. Hence the negative growth not working etc. Custom races as such makes a huge difference for a competent human player vs an AI.
Takes approximately five minutes to fix, provided one has spent a couple of hours learning the structure of the xml and understands how the game works. Give yourself maybe half an hour to think of suitable bonuses, though tbh if it takes more than 10 you probably don't understand the game well enough to be making changes to it.
-Malevolent is the ideology of choice. Death furnace is an insane raw production boost when built correctly, and nothing in the other trees comes close. (except for the flip thingie in Benevolent maybe) The AI has no clue how to utilize this stuff correctly, and is as such heavily penalized compared to the human player.
The trees are actually pretty well balanced already tbh - there's about a dozen abilities which are either too poor or too good, but fixing them is again a five-ten minute job. Death Furnaces, for example, can be brought broadly into line with the other ideology traits just by nerfing the level bonus down to 1%/level. Much of the rest of the three trees can be made workable just by flipping a few flat values to multipliers and visa versa, or just changing how many planets are effected.
-Weapon min-maxing is out of whack. The right specialization techs, coupled with the right modules, makes the fights ridiculously lopsided. The AI can't compete at all. The basic resource less weapon modules should probably be nerfed. They are way too powerful for their cost. Boosting your weapons that much should cost strategic resources or something to balance it. Again, massive human boost if you design your own ships properly, AI should not be expected to compete here in my opinion, the balance is just off. This should be the place you go to to defeat the AI as you increase difficulty.
Took me most of the evening one day after work a couple of weeks ago to plod through this - we'll call it four hours. Which included writing up the spreadsheets, changing the necessary values, re-balancing Defenses in line with the weapon changes, adding in an extra 9 weapons, figuring out how the localizations work, and re-balancing the blueprint defs.
-Endless projects. Birthing subsidies is too powerful, and the basic mechanics too weak. Same with influence. You don't even need those fancy culture buildings, just raw production and a project. This is probably the most broken part. When a birthing project creates more citizens per turn than the ultimate Yor assembly line, something is very wrong.
Takes less than five minutes. Just change them from multiplier bonuses to flat at a 10:1 or 20:1 scale, so that 1 manu gives 0.1 research/econ. Influence can be given 0.01; birthing subsidies 0.1%. The real problem with projects is not the conversion rate, but rather a matter of manufacturing, research and econ bonuses being silly-plentiful and it not being particularly hard to get Food over 100. I suspect the devs thought people would build 2, maybe 3 farms, rather than 8 or 9. They need to either harshly limit food - so getting over about 30 population is nearly impossible - or aggressively slash building bonuses; either would help the game enormously (I chose the latter).
Seriously, none of the above are big issues. This one:
-Tech trees needs rebalancing, both in cost and power. Thalan tech compared to the others is insane. I think the Thalan design was intended to be balanced with the negative growth, but that essentially does nothing due to abilities being useless at the moment.
Is just about the only time-consuming thing on your list, and that's largely because there's ten files to go through. Though tbh, even in this one's case it's not actually hard; most of the big advantages that the Thalans get are just OP buildings, which it's very quick and easy to change to something more balanced. You can deal with the worst-offending bits in the course of an evening - which again includes taking the time to spreadsheet them - and it might take several hours to do a proper re-balance.
In sum, this whole list is about one weekend's worth of work. For some context, when I was modding Victoria 2, getting the game to a remotely balanced state took around 2 month worth of man-hours, and I suspect the total time sunk into the project by the end was probably nine months to a year. Most of them mine; I was working on it 18 hours a day for about three months at one stage, and the mod was in development for three and a half years with a team ranging between 2 and 10 people. THAT was a game with some serious balance issues. GC3 does not begin to compare on that; what we have here is a largely working system with some fairly minor balance problems and a strategic AI that can't play it.
There are some serious structural issues in the game mechanics, which will take a lot of time to work through - I touched on a few in the post above, but also things like the way growth works, the fact that building bonuses are too big, the fact that level bonuses are insanely overpowered compared to the already-overpowered buildings, the fact that LEP is presently little more than a flawed concept poorly implemented, and the resulting imbalance between 'tall' and 'wide' - but nothing on your list really qualifies for that; it's more like one day's worth of work for a junior scripter. The strategic AI scripts are a way, way bigger problem, which is way, way harder to deal with, and will require way, way more work. Worse, fixing some of these real problems actually requires fixing the strategic AI - to introduce any meaningful penalty to expansion or reduce building output, for example, will cripple the AI in it's present form and basically requires re-writing all the scripts from scratch (which, incidentally, took around 6 hours to do, including expanding it from about 20 scripts to about 200 - probably about the same amount of time it'd take to do the biggest item on your list).