1. Duplicate resources on the same planet do nothing. (Snuggler Colonies, Hyper Silicates, etc)
2. Artifact Anomolies do nothing but flavor text for research. (Capsules give 15% tech)
3. Resource hexes with special abilities spawn too random (like +3 social manufacture on Homeworld) but you can't build anything on it (Except Deep Core Mining) but you can't build Deep Core on your homeworld. (And it does NOT apply to Space Elevator) Very frustrating.
4. Random techs (Like Specialization for Hull Capactity) are 70 turns to research where the others in its group are like 26 and 56. Why?
5. AI techs seem out of control. Trading with Alterians and Iconians and they are like 30 techs ahead of me at turn 60 in the game. What?
7. Colonizing seems out of control. Focusing a game purely on colony ships (about 5 turns to build) I managed to get 10 planets. Snathi and Thalan and Drengin all had 15+. What?
8. All generic ships in shipyard all cost resources to build. No option for non-resource (Antimatter/Elerium etc) ships. You -have- to custom make them at the beginning.
9. Always around turn 50 I get 2-3 AI races declaring war on me. Even with diplomacy feats and diplomacy techs taken. Never had this issue in v2.0 did they tweak the angry UI?
10. Anomolies and planets and resources seem way too random. 1 game I have 50 anomolies around my capitol the next I have 5. One game I have 50 duratanium/thulium/promethium around my area, the next I have maybe 5. One game I have 10 level 15+ planets (5 of them non-radiation Precurser worlds immediately habitable) the next I have a total of 6 worlds around me all less than 11. I have no idea what dice rolls are being used for map generation, but for the love of god.. please normalize this.
11. Some AI are super colonize-y and will spam planets and have 20. The next AI i meet have maybe 3, even with worlds around them. What is going on with this?
2) Artifacts do rarely reward finishing the current tech research (sounds like percentage needs to be changed) but mostly give large currency reward. Capsules do very often finish 15% of the current research - otherwise give small currency reward.
4) There are a number of typos in the MasterTechDef.XML file related to various choices specialty tech choices - I have found about 6 more after someone posted a few fixes to several others in that file. Stardock will no doubt fix this soon.
5) Can disable tech trading at the start of the game - remember the AI is much smarter now and running at anything above Normal is probably not advised till you are used to all the new changes.
9) Yet to see mass war declarations but if you have no navy they probably are now more likely to attack you if they are aggressive by nature.
10) Certainly there seems to be some issues with the galaxy random generator - Number of planets can be fixed with the Mapsizedef.xml changes. Hopefully Stardock will look at the galaxy generator code and make it more like it was before Crusade but remember you need access to every difference resource possible including the new speciality strategic resourcs to properly play the game. I have been stymied by not having access to Antimatter to make Starbase Markets to improve my economy at the start of the game.
11) With the low default growth rate (0.1 per turn with no bonuses) certainly mass colonization at the start is not bad strategy if you don't get overextended or neglect having any kind of military fleet or defenses. No doubt the AI needs to be tweaked some more but it apparently on purpose the AI by default plays a more aggressive game.
Remember the expansion primarily was focused on developing a more advanced 64 bit gaming engine that allows for better multicore CPU support to allow for larger maps and for faster turn execution (unlike most of the current 4x strategy games that are very single core CPU limited by using an older game engine to run the game on - ie Stellaris etc.). They also changed quite a number of game play decisions to appeal to the more casual strategy gamer because they after all need to make money on selling games even if you happen not to be one of those users. Most of that effort has been successful but like when the version 1.0 of the base game was released there are still issues with XML file typos and tweaking to the UI and various design changes that need to be finished. And presumably everything is ready for the game to be modded to make various changes to the default behavior of the game to accommodate players that might want a more advanced game experience as well as ability to support customization of civilization designs and maps.
In some ways you have to relearn how to play the game because it is no longer the same game that existed before version 2.0. This can be annoying and frustrating but hopefully it will be worth it later.