Here's my partial list:
Additional Resource types (money, SPice, etc.) added via mods. I think SE4 is close to being able to Mod the DUNE universe - SPice would be part and VERY rare, but you also need the ability to have an AI race that would act as Navigators. SHips would have no ability to warp - they would have to load aboard guild heighliners (Obviously this would need REALLY big ships)
Obviously, Intel needs to be greatly improved.
Saving Game in turn (as others state) needs to be in an upcoming patch. I spent 2 hours doing a turn the other day and got a phone call that made me run out - I left the PC on but it locked up while I was gone
I would like planets to actually ORBIT the stars in a system. Maybe not in Real time, but they would move around a bit in between turns.
MOre Strategys that work. Abilityt o have sub-fleets (aka Task Forces, within fleets with different orders).
Sats should spread evenly around planets!
A note taking system built into the game - I want to be able to add notes to Races, planets/systems, fleets, I forget sometimes what my long term goals were for any given "thing" and this would help facilitate that. Especially in PBW, where some turns don't run for 2-3 days. I don't think that would need to be incorporated in the .GAM file obviously.
Edit Messages already sent and be able to send multiple Messages to other players.
Ability to export current tech levels. (the list that is, so I can print) Maybe even the ability to compare to a Partners for trading purpose.
More soon... I'll probably have a TON of more ideas when MOO3 ever finally comes out...
Binford