The PQ resetting to base value on reload is the second most annoying glitch I have encountered and would like to see fixed.
A couple of easy ones that will just be xml edits probably (but I guess doing them myself would invalidate metaverse games):
VR Centers only give +40% Morale, whereas Zero-G Stadiums give +55%
Advanced Farms only give +8Mt Food, the same as their predecessors.
Not had a chance to confirm if the next one still exists in v1.0x (as don't like having to reload due to PQ reset), but building the No Mercy Invasion Center caused reproduceable immediate CTD whenever an invasion was attempted after it was built. Simple answer is not to build it of course, but if one of the other evil races built it would the same happen if they invaded one of my planets? Also if the planet it was built on culture flipped to me, would the error re-occur? If so, it is a potential game-breaker!
AI behaviour - they're still building cr@p on resource bonus tiles (had a farm on a +700% manufacturing bonus tile on one planet last night, with 4 factories built elsewhere)
Finally a couple of things to reduce micromanagement that would be nice to see implemented:
The ability to fleet up more constructors, to save having to wait for 14 (when building an influence starbase) to move individually when you give the stack their initial movement orders. Setting the logistics value to 1 for constructors would achieve this. Is this possible? Obviously this could allow for a potential exploit by fitting a huge hull with a constructor module and then adding weapons, so I guess there would need to be a check that all weapon values were zero in there aswell - still, it would make life easier.
And on to the most annoying thing in the game... please make the Esc key always replicate the action of clicking on the "Done" button. It does for some screens (e.g. GNN News, Tech screen etc), but when you hit Esc with the planet window open, or the relations screen, or the economic screen you just get the options menu. Most frustrating!
Got to be a great game if it's a minor UI glitch that annoys me the most.