Something i'd like to see that wouldn't be too hard to do, is give each species a couple beginning level techs. Each species would have different techs appropriate to their style. This is mostly a way to actualize the species concept. For instance if a species is described as living underground give them "Subterranean Construction" right from the start.
This is something which would only make a difference at the beginning of the game. We should decide if different species have bonuses and penalties which cannot be replicated or if future techonlogies would allow anyone to learn the bonuses of other species.
It seems that now every species can and does live underground, since "Natural Tunnels" is a planet special. Maybe a species which lives underground should start on a planet with tunnels. The environmental preferences determine starting world. (Maybe some species should be claustraphobic and not be able to make use of the natural tunnels special.)
There is technology to allow terraforming, changing the planet. But should we have technology to allow the species to change? Doing genetic engineering to change the species. There are psionics and cyborg technologies already in the game. Are these the same as a species staring out as a cyborg or psychic?
My main point is that species specific abilites and researchable technologies could easily overlap. As far as I know a decision has been made that all species have the same tech-tree, so it seems that species abilities should be different to technologies and should therefore not be replicated by technologies. Currently only environmental preference and appearance are different between species - this makes game balance easier to acheive, if there were an equal number of each planet type (which I think there isn't).
I think a good species research bonus would be to have a bonus (cheaper research costs or minimum number of turns) to a specific area of the tech-tree (for example ships). This would allow a warlike species to stay warlike the whole game. I think it is important to have species bonuses which are not watered down by the technolgies gained throughout the course of a game.
<<Edit - shouldn't this thread be renamed bringing balance to the species?>>