I would love to see each of the minors have some unique technology or civ-wide bonus that you automatically gain if you team-up with them (unbreakable alliance) but there is a 50% or less chance of getting if you conquer them. I think that the bonuses shuold be simular to anomoly bonuses x5 or simular level (i.e. 5-10% bonus to economy, soldiering, etc or +1 speed to all ships.)
It would give a reason to care about them and try to woo them.

I agree with Scintor and Lord of Ruin, those are fantastic ideas for minor races and would make them much more fun and interesting. Presently they are only there as another way to get some more econ/industry capitals, trading and bully for some techs. It would be great to be able to have them join a major empire peacefully (maybe when you are in an alliance, and having a high diplomatic ability would increase the speed in which they join you) and grant a small empire wide bonus, such as

Dark Yor - +10% weapons
Jessuins - +10% Morale
Snathi - +10% Military Production
and so on. I think the expanson of minor races really is the logical next thing to include in an expansion pack (after Dark Avatar, if another is made).

It could potentially fit with the storyline (someone trying to create a new coalition to oppose the Drengin).

It is easier to add minor races than major races (you can only play with 9/10 opponents, so adding more major races would not be as good, as you could not play with them all at one time). With minors, this doesn't matter (maybe even have another civfanatics contest to include a minor race??? ) Being able to select amount of minor races in the galaxy would be good (even just a scrolling bar).

No need to create a totally new AI script for every minor race, like with a major race (althought it would be good to have maybe 2 or 3 minor race AI scripts. Like aggressive expansionist for the Dark Yor/Snathi, Defensive for the Akilians etc)

Much more fun to play with more intelligent opponents (minors usually act pretty dumb)

That is why I think minors should be the next to get a workover.

I personally enjoy the minor races. They add some variety and can even be a tad unpredictable. For instance I had been losing a war to a three alien coalition. I finally convinced them into a peace treaty. My empire was in serious shambles. So of course my neighbors the Akillians declare war on me and finish me off in a few short turns. That was a little akward.