This is a "short" list of the glitches, bugs and exploits that I've come across since upgrading to version 1.1:
1. Needs the ability to set targetting priorities for combat. When the enemy has 8 - 12 tiny/small ships in a fleet and 2 or 3 large/massive, I don't want to pick off the small fodder first, I want to take out the big ones that can actually punch through my defenses. (Heh, maybe the AI is smart enough to make use of "chaff" ships)
2. Economy fluctuates for unknown reasons. i.e.: I make say 9000bc one turn, 2 turns later I'm making 7200bc, I haven't noticed anything that may affect it either. When I look at the curve on the graph for economy, it still slopes at the same rate, but sometimes just drops a few thousand bc every once in awhile and then returns to normal.
3. Haven't read too much into the latest manual, but the original said influence and ownership are not the same. When looking at the ownership, the ratio of your influence to their influence (The number in parenthesis next to influence), only goes above one once they are in my "territory"
4. Miniaturization is still glitched somewhat. If I research few miniaturization techs, build one ship design, then upgrade it each time I get any form of miniaturization increase, I can fit significantly more components on it then if I just started a new design from scratch. (Cargo hull class HyperWarp MkIII is listed at size 11, yet only takes up 9 if model is consistently upgraded, but will have the listed size of 11 if started from scratch.)
5. The Doom Ray still shows up as "blank" square in the ship designer.
6. The cost, size, and damage of the doom ray makes it almost worthless once all weapons techs are research. On a massive hull, it takes up 14 spaces, does 22 damage and costs 150. Where as the Blackhole Eruptor costs 160, does 25 damage and takes up 12 spaces (maybe 13, can't remember exactly). Then the Blackhole Generator costs 100, does 16 damage, and takes up 11 spaces. Ignoring cost, the Blackhole Eruptor has the best damage:size ratio, and the doom ray has the worst damage:size ratio. (If the miniaturization exploit mentioned in 4 is used, subtract 2 from each of their sizes except for the Blackhole Eruptor which goes to size 11 from whichever, 12 or 13, it is listed at)
7. If a game in the beta versions was started, then you upgraded to v1.1 final, you couldn't remove starports. Not a big deal, but I don't want a starport on a class 4 planet since it's worthless as a ship builder.
8. I've noticed that "Gifted" A.I.'s seem to do much more better later in the game than even more intelligent A.I. computer players. Having more "Dumber" A.I. causes a lot less lag when turns are ran as well.
9. A.I. still doesn't understand how to use every building to its potential. A stock market has a small morale and influence bonus, so instead of the A.I. placing a farm or factory over a morale/influence boosted tile, why not put the Stock Market over it instead?
10. A.I. still doesn't quite grasp that it can't put the equivalent of 13 farms on a class 18 and have maybe one morale boosting buildings on it and expect the planet to be happy. Get the idea?
11. Having a planet quality bonus selected in your race abilities only adds the bonus tiles to newly colonized planets. Even though conquered planets, using military or influence, have the listed class rating with the bonus added, they still don't receive any more tiles. (i.e. With a +10% bonus, class 18 planet goes to class 20, but still only has 17 or 18 tiles, that's including the initial colony.)
12. The U.P. issue that has races donate 'x' amount of bc, depending upon which one is elected, doesn't really state that it adds a morale boost. (1000bc = +50% morale that is unaffected by population)
13. The Secret police center's stats say it gives a +20% boost to base morale. This makes it look less valuable than even a entertainment network. When it uses "base morale", does that mean it's unaffected by population?
14. Neutral races are said to gain unique weapon and defense technologies, I have yet to see any.
15. Neutral races are also said to get a break when purchasing ships instead of building them, still don't see that either. I think their might be a slight reduction to purchasing social projects though.
16. Looking at the stats of other races, they have some bonuses, and I am sure I am not alone in this, that I have no idea what they do or affect. (i.e. cabinet, crime, interest rate etc. etc.) I think the Interest rate is related to purchases mentioned in #15 since I noticed a +25% once I became Nuetral.
17. No bonus income is apparent when building each ethical allignments Hall of Righteousness/Nuetrality/(Don't remember name of evil one).
18. Have seen the A.I.'s influence plummet for no reason. Checked for destroyed influence miners, but nothing changed their either.
19. Auto-Explore has improved some, but it frequently skips territory close to home. Tends to favor flying to the north or south edge of whatever side of the galaxy you're on and then fly to the other side, then exploring in a "striped" pattern.
20. A.I. seems to know where all of the resources are initially.
21. The trade routes max. value and current value are always the same even when a route starts over (i.e. Made a short 56 turn route, started at 19, went up to 58, then went back to 19 once route started over, yet it never said the max value was 59 when it started over, put it back to 19)
22. Trade route values need some sort of explanation. I got more out of that short route mentioned above, than a route that had about 250 turns. The short one went capital to capital, but the long one went farthest starport to furthest friendly A.I. starport.
23. Low morale doesn't seem to bother the A.I., or have any chance of causing revolt. Planets will have 23% morale, and the A.I. still keeps throwing on farms. and not building any morale assisting buildings.
24. Current version 1.1 influence ratio (number in parenthesis next to influence) for an A.I.'s planet with it still not defecting, 77.2, scary, right? Although, beta 3a set the highest record for me, 1000+ and still no revolting. That was when I had every planet except for 3 or 4 and was waiting for that one remote A.I. planet to defect before moving in to take the last 3 of my soon to be former ally's planets.
25. Game still crashes on Autosaves about 15% of the time.
26. Game crashes sometimes when A.I. surrenders to you.
27. Unlimited ship movement in "one" turn still works. When a save game is loaded, all of your ships will have the same movement remaining from when you saved, but when you end that turn, no time actually passes (No production or research occur), but ship movement is restored. Is possible to rinse and repeat unlimited times.
28. Weeks aren't always 7 days long, sometimes they go as high as 10 days! Calender also doesn't take into account leap years.

Heh, nothing major, but kinda funny.
29. If Information warfare is selected, and the battle is lost, the amount of population that defected is still added to the remaining population even though they were supposedly killed.
30. My ship attack total 236, their ship, defense total 0, have done less than 10 damage in one shot sometimes, even did no damage two of the times.
31. My ship defense total: 120, missle defense 80, their total attack: 24 (all missle), still does damage against me about 20% of the time, does full damage half of that time usually.
32. A.I. complains about my military buildup and starbases, but I can't do anything about them leaving their fleets next to planets I conquered with influence or about them building influence starbases next to my planets.
33. A.I. values mining starbases to much. As in I tried to trade for an empty influence mining starbase, they still wouldn't give it up even when I game them EVERYTHING I had. Obviously I wasn't going to give them every tech/planet/ship I own, but you'd think they would at least see that as a good deal.
34. A.I. considers influence points in trading as almost worthless. (10000 influence points was worth about 9bc)
35. A.I. thinks their money is worth far more than yours. (A.I. will give you 9bc for your 100bc, or will pay ~400bc for a tech that would cost you 2500+bc to buy from them)
36. PLEASE give the option to make some fonts appear bigger, I have a hard time reading the fonts that are REALLY tiny, and I know I am not alone in this.
Anywho, my fingers are tired now, I will add more if I find others, a lot of these are just complaints, but I feel the ones I mention are gameplay issues that would make the game feel more balanced if adjusted some.
Hope I get SOME feedback!