All this crossover hate from people who liked my crossover? Intriguing?
Seems more like you hate stories where character X is mysteriously appears in parallel universe Y and follows the plot of story Y with absolutely nothing to differentiate the fanfic from franchise Y aside from the insertion of character X. But everyone knows that's how you create a bad crossover anyway, so really you just hate bad crossovers.
Good crossovers involve the merging of two entire universes, or a canonically plausible method of inserting a character into an alternate universe while maintaining a unique plot that is heavily influenced by said characters insertion. I can give you a list of great crossover fics of all stripes that I know you would enjoy.
And honestly, with science fiction or a universe composed of multiple realms, it's really not that hard to toss in another planet or realm and have it perfectly believable. I'm breading an awesome fanfic that crosses over Halo and My Little Pony. Badass Twilight Sparkle... <3
Also, I can't seem to write for Mass Effect any more. I just can't. I think that ending killed any and all inspiration I might once have possessed. So now I'm writing a first person quasi-SI MLP:FiM fic. The first four chapters are already up on FimFiction, so I'll put it up here soon.