Unless you purposefully pick out identifiable traits and try to tie them into the real world as a poorly disguised inside joke, I don't see anything wrong with making black orcs tougher yet possibly not as smart as goblins or whatever. In lord of the rings the black skinned/painted orcs with the white hand mark on them were stronger. bred that way out of the earth as a twisted form of elf.
There is no way to avoid having characteristics that set races apart and personalize them in a fantasy world. Players will want to look at a race, read a short description and have a feel for what its all about. So having intelligent devious yet weak goblins or gnomes breed with a big nasty troll to create a half breed that's not quite as large as a troll, but is more cunning and agile could make it a desired pairing.
If you go into detail as much as the "sims" game goes to personalize every character in the game, and then breed them together it would be way too much micromanagement for a rts.
What you could do is develop a combination, take the trolls and goblins base hereditary stock, and then experiment with percentages of lineage from each type to end up with a desired set of characteristics or stats in combat. Then once discovered you could apply those base races as resources that you must combine in the correct parts or fractions thereof. And as long as you have the right mix of the base breed you can create a stock or barracks of the hybrid. After that they could just breed with eachother.
I think this type of game could be fun, as it may end up like spore but instead of one race you have various genetic branches you can explore.
I think what others may have posted worries about is a deep seated ethnic slant to the game corresponding with real world peoples and cultures.
I don't think its an issue as its a game, and you would have to go out of your way to pattern in such slights.
If you are familiar with the wheel of time series, the trollocs in those books are humanoids with various beastial mixes to them. Horns, feathers, claws, hooves and all in a humanish looking form. That may give some inspiration.