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Maybe this is close to what you looking for?
I really do wish there was some sort of dominance-recessive system for the genes.
Thinking about it, I don't think it would require the overhaul I'm asserting here. I think a weight value could be added to any genes that conflict, and then take that into account instead of randomly picking one of them.
Building an in-game framework that allows you to create custom genes would be tricky. That's the overhaul I was referring to, but I don't think it's nearly as dramatic as I initially thought.