Science things:
1. Faster than light travel
2. Random bits of magic (cap ship abilities especially advent)
3. Use of antimatter as a power source
4. Faster than light travel!!!!!!!
5. Faster than light travel!!!!!!!!!!!!!!!!!!!
6. What is a phase lane anyway?
Edit: 7. Things generally not orbiting
General things:
1. Stars FAR too small (perhaps this should be science as well)
2. Too little variation between planets
3. Too little variation within a planet (a whole planet a desert??? even at the poles????)
4. Upkeep system (mentioned above)
5. Stars FAR too close together
6. All races have basically the same structure in their fleet
7. Vassari not massively overpowered (after millennia of development)
8. Ship movement (in a gravity well)
9. Orbital civilian structures (OK trade ports and shipyards are sensible but really why not have labs and broadcast centres on the planet?)
SUSPENSION OF DISBELIEF
Edit: Finally I have to disagree with this:
-----"I don't see how the 'ten-millennia journey' could be realistic. That seems like a little too much journeying."-------
This is the only way to travel between galaxies or even Solar systems in reality. If we ever make to other stars or galaxies in reality we will have to travel at (just) sub light speeds. Hundreds of Millennia will pass to anyone moving at slower speeds (for longer journeys) and centuries on the ship(s) (look up time dialation). END OF EDIT
I think that having these things in game is fine. Perhaps there should be a note in the manual saying something like "This is not possible as we currently understand things" next to appropriate entries?