I did a thread in Ntronium forums with my first suggestions, here it goes:
http://ntronium.com/simplemachinesforum ... opic=409.0
In summary (sorry, long post):
- Toggling planets in the planets list should keep the last tab active
- The fleets list should be enhanced to be able to sort by class. And by the way we should be able to merge ships by class.
- The planets list should be enhanced to include the non-colonized planets
- The game must have an intro
- You should consider changing the colony glowing thing to something more functional, maybe static and with a stronger color.
- The ship routes need to provide the option to switch them off. Maybe an option to show them when we click the planet where the ships are headed to or where they come from.
- Right clicking in a tech while in the diplomatic screen should present the technology information
- Mine Complexes should present the amount of base production they add when constructed
- Diplomacy deals are sometimes very odd like some race offering $1 or $1 for 3 turns, these are very odd deals, you should consider removing that.
- Many times a 100% deal is rejected by a race with a counter offer that does not include the initial offer. If this is a feature at least we should be informed why they didn't accepted the first deal in the first place (maybe something like: "we have our reasons").
- Races reject gifts (tried with techs), and keep constantly rejecting all gifts. Tried with 2 races. And in the end they get offended

... bug or feature?
- I have no idea of why a race is hostile towards me (there are no modifiers or historical records). I really miss something like Civ4 positive and negative modifiers. If I recall correctly GalCiv2 also provides this.
Other topics addressed here:
- Auto-transport Pop thing: No, shuttles are elegant. Keep it as is.
- More options to custom maps: Yes, definitely.
- More techs: Yes, important.
- Ship costumization: No. Or else is SE4 or GalCiv2, has some have mentioned (let's try something different for a change).
- Different planet sizes: Agree.
- More ships: Yes, make them more different for each race
- Bureaucracy: I like it, similar to Civ4 expansion costs (makes sense). Must provide structures and/or techs to counter that effect (like courts, special police or new forms of government)
- Fleet lists and Colony lists needs upgrading to sort all non-colonized planets and show ships in a more structured way
That's it for now, more to come...
I'm still in the middle of my first serious game ... maybe my auto-transport opinion will change

anyway remember that if we need to come up with fantastic turnarounds to something is because that something is flawed in the first place.