I'm sure most of this has been mentioned but:

1. A 'Launch all button' for each planet and one for the whole empire

2. Fix the star and planets so they look realistic. That is, get rid of green/purple stars, have some binaries, make the Red stars huge and have no habitable planets, and white/blue stars very small, with 'cold' looking planets.
Also make it so that all habitable planets look habitible. As one guy said, I have seen systems with 'planets' that look like earth and 10, 12 etc planets that look like barren rocks.

3. Make it so you know you are at war and who with (icons on their ships)

4. When you get a GNN report and click 'Go To' the planet in question should be removed from the list when you press done.

5. Have some indication of tech worth (in beakers) to help with trading.

6. Make it so that if I give laser III, for example, to a race that has only laser I beforehand, they can't research laser IV until they get laser III. That is, don't allow the CPU to just jump each other miles up a tech tree without doing any work. On the same vein allow a 'no tech trade' option.

7. Make it so that it is easy to see a planet's max pop.