I would recommend Sins of a Solar Empire, only because I haven't played Sword of the Stars. Sins is a great game, just requires more strategic thinking than your average RTS I've found, considering you have more ground (or rather, space) to cover, and a strong economy is key to survival! Plus it's always refreshing to see your sworn enemies' planets getting nuked, is it not?
Then I phrased it badly then . But seriously, I probably could've said it better, so I will:
I recommend SoaSE, though I have never played SotS so I can't make a fair judgement.
Though to be honest SotS does sound intriguing now that it's been mentioned (never heard of it before now to be honest)