1. No Governor Leader, admiral or land battle leaders.
Both in experience (XP) and the commendations on each leaders. I always play KOEI's game, like Romance 3 Kingdoms series , Nobunaga Ambition etc. by using the leader xp and commendations the game will not be bored . And with additional story lines or relationship with this leaders (like in Total War/RTK), this game will be the greatest Space strategy....
2. Bad Srategic AI
This game AI is really boring. AI will not build up Large Army to invade and rarely use full fleet. What makes the Master Orion III fail is the AI is so stupid. I played about 200+ hr now and i am longing for big invasion and suprise attack. I remember the first time I play MOO II that game was absolutely made me crazy, couldnt sleep for 2 days 
3. Space Battle Sequence and control
Its pretty fair atm. Although i miss some of MOO II user control.
4. Land Battle Sequence
This game need rework on this parts, I just dont feel the right Atmosphere from it. If only the developer can simulate this part on animation like that in space battle that would be great.
Hope the dev will hear this....and updated this game asap 