I will compare FreeOrion to Civ4, since this is the only other strategy game i know.
What i think should be changed generally:
1. No species should start with extra ships (Eaxaw and Etty). Even with the nerf to Laser 3 (Eaxaw) it is still possible to conquer AI home-planets with those starting ships. Isn't it sufficient to give them free techs? This could be done with every species similar to Civ4. The free starting techs could encourage different playing styles (expansive, agressive, defensive, etc).
2. "Narrow planet tolerance":the game depends too much on the galaxy formation (=luck). If there is no "good" planet close, even after researching Orbital Construction, you are screwed.
As in Civ4: the start of a game is crucial. If you first have to research 86RP/6T, then build an outpost ship to connect...you are just too far behind. Teching to Orbital Habitation would cost 624RP

I understand the galaxy formation is somewhat limited (ie the problem with home-worlds spawning too close), but perhaps something could be done here, ie. ensuring at least one "good" planet nearby?
Or perhaps changing the system: suitability poor -> good always gives a positive pop and the pop-cap is increased with techs?
3. "Xenophobic": i generally dislike this addition. Invading natives early on is useless. If not completely removed, the negative effect should at least be smaller.
In my latest game i had 3 Trith colonies and invaded one native. My 3 Trith colonies lost combined 32pop and 8.6PP. The native planet added 18.7pop and 9RP.
Trith now combines the worst combination: "Narrow planet tolerance" and "Xenophobic".
Eaxaw's starting ships encourage aggressive play early on. But unless you conquer a home-planet, invading a native/Ai colony gives you the same effect as described above.
To sum it up, I think all species should have the same/similar conditions at the start of the game.