Okay, one of the key things, in mind, that separates out the bad from the good is the way the story stitches the two (or more) worlds together. Can you see the seams? Do they stick out like sore thumbs? Do you twitch because the characters take a while to introduce themselves?
Like, one thing that I find really annoying when reading crossovers are the long, boring explanations of one fandom to another. ("Hi! I'm Buffy, the Slayer. I kill demons and have super strength and heal faster.") It's generally unnecessary, because it slows down the action and draws attention to the fact that these fandoms don't mesh together naturally.
One of the really nice things about fusions is that you don't have that same problem with exposition. House doesn't need to learn what the Galactica is and Rodney doesn't need to have mutations explained to him. It removes that need for exposition.
Anyway, the point of these ramblings is to say, I think, that generally it's easiest to assume that your reader knows all the fandoms involved from the get go, so you don't get bogged down with the boring shit.
P.S. And no, I'm not thinking about these things because I'm writing a sequel to High School Is Not Another Name For Hell. Why do you ask?
P.P.S. This is not a GIP at all, either.