My view on this hasn't changed since Stardock upset some people by bringing the Crusade DLC to GalCiv3:

If you're going to have Minor Races, don't do it the old way where Minor Race sits and drools on it's Class 16 planet, never expands, gives you whatever you want and when you get sick of them, doesn't put up a fight and dies.

Give some abilities/skills/resources only to Minor Races and, obviously, make them un-tradeable. If that Minor Race dies, that ability/resource/skill dies with them. Make these things that only Minor Races have gel with/buff up Major Race abilities/resources/abilities.

One example, the Antidrengin Minor Race have a Very Angry Ability that buffs up the Angry Ability. You're an Angry Ability Major Race. Your small beam warship (which you get from the Angry Ability) gets a larger beam and more hit points when you meet and make nice with the Antidrengin. However, your ship loses that benefit if the Antidrengin are killed by those pesky Alterians.

Another, the Zomba have a skill in mining resources that allows all resources obtained by you to be mined at double speed and double return...

I'm sure others could come up with heaps of examples of Minor Race skills that would be useful to a Major...

Personally, I would like to see minor races be handled more distinctly than major races than what we've done in the past.

That is, a minor race is basically a super colony world (if they're in your territory) that has lore and potential quest related content around them.