I've noticed all of those bugs except for number 5 as well... I have some to add to this list though...
7. Despite one of the fixes being listed as improved A.I. usage of tiles on planets, I've actually found them to be dumber than before.
a. A.I. puts 6 Advanced farmings on a planet with no morale boosters except maybe a stock market.
b. A.I. upgrades buildings with soil enhancements/Habitat Improvement/Terraforming for some reason
c. A.I. upgrades buildings to the same building (My personal favorite)
d. A.I. only seems to recognize manufacturing and research bonus tiles while ignoring the rest.
e. A.I. puts a Starport on every planet, but sometimes forgets to put manufacturing buildings on smaller planets.
f. A.I. doesn't always build on every good tile.
g. A.I. still fails to understand how to specialize planets.
8. The 4 starbase per sector limit works, but only for the player it seems. My personal favorite was 6 A.I. influence starbases within 4 tiles of each other all in the same sector, and all of them empty...
9. I've seen the A.I. build mining starbases where their isn' t a resource, I have the save game to prove it if you want to see
10. The A.I. complains about starbases I've built. Normal, but complain about ones I've built 2 sectors away?
11. A.I. can complain about starbases and make threats, why can't we complain when they build an ungodly amount of starbases near me?
12. After the A.I. destroys a starbase or mining facility, it will attempt to attack it again for the next 2 - 4 turns even though it's already dead. (I know this because the camera zooms to where the A.I. killed them and is still sitting there trying to kill it again.)
13. To upgrade one starship costs, we'll say, 1000bc, having 10 of them would make it cost, 10000bc, correct? Wrong, if you click on the upgrade all, it would probably cost around 12000bc to upgrade them all at once.
a. To get around this, just upgrade each ship individually
14. Miniaturization is screwed up. If you upgrade a design after researching miniaturization techs, and have it keep all existing components, you will notice the normal hull size increase, but the component size will also seem to get smaller by the same amount of miniaturization, essentially doubling the affect of miniaturization. (i.e. How else can I stuff 15 Black Hole Generators, 10 Ultimate Invulnerabilitys, 8 Zero-Point Armors, 2 Aereon Missle Defenses, and 2 Hyperwarp Mk III engines on one Huge hull!) Although, it kinda balances out because the cost for using the bug and fully utilizing the space it enormous! This doesn't work if building from a new hull!
15. A.I. builds more freighters than it has available trade routes, understandable, except that the A.I. keeps sending the @#$%^&!! things around trying to make new routes when it can't... Although it does come in handy when one of their old routes is destroyed since you won't have to wait more than a turn or two for a new route.
16. A.I. ignores morale a lot of the time, but despite their planets having 41 billion people and a 23% approval rating, why don't they ever revolt?
17. Advanced farming STILL only gives 8 food/week, same as intensive
18. Reducing the costs of techs on the normal rate may have been a bad idea since most of the A.I. players and myself were able to get everything within 8 years.
19. In my opinion, the costs of the Stock Market and Industrial Sector are WAY higher than they should be, but that's just my opinion
20. Political Capital doesn't double influence, just adds the same as a Cultural Exchange Center. Only other advantage from it is that it adds 50% to morale. It also doesn't cost enough in my opinion.
21. The U.P. tech sharing issue is bugged, if I vote for 3 shared techs, and say 1 shared tech wins, I still get 3 techs from each race! Also, no matter how far ahead or behind I am in research, it still says the other races cleaned up even though in reality I did. (Especially when given Industrial Sectors and Supreme Miniaturization!)
22. I build a scout with enough sensors to see 21 parsecs, yet it only goes to 15, I build another one with 23 parsec scanner range, still only 15 max, is this intentional?
23. The desctription of the Galactic Showcase says it increases the cultural influence of the planet it's built upon, but instead adds a 25% bonus to diplomacy...
24. Get rid of or change the Galactic Guidebook. By the time someone actually builds the thing, all of the anomolies are already found, at least in Metaverse games.
25. Have and option for influence not cause planetary revolts if victory by Influence is not checked, this way one can't get a "Military" conquest by subverting everyone else culturally.
26. Raise the natural pop. caps, or have the Soil enhancement trees raise the natural cap. I hate having a little class 5 planet and not being able to get it's population to the 5 billion of the initial colony
27. Having Planet Quality bonuses are worthless after every planet has been colonized since conquered planets don't get that bonus.
28. Abandoning planets permanently removes buildable tiles that were created from Soil Enhancement and the other terraforming techs.
29. Abandoning a planet with a Super Project or Galactic Wonder prevents you from building it again even though you don't have it anymore.
30. The description of the Omega Research Center doesn't clearly state wether it gives the bonus on the planet it's built on or on an empire scale.
31. A.I. tries to trade some weak tech like Miniballs II or Missle Defense theory for my Quantum Driver III or some other really high weapon tech.
32. A.I. doesn't research any of the sensor techs until it runs out of other stuff to research
Anywho, I am sure I can think of more, but I am typed out... And yes, I am VERY long winded as you can all tell!