Think it through as well - what do they look like, how they attack, how they act, and so forth - into details and all. If it relates to a 'real' animal or thing, look into that as well.
Not nesserary, but also, try to have the Pokemon 'original' - as in that the official Pokemon don't serve the same purpose as it, or the such. Or, try not to make a Pokemon that is too similar to other ones for the sake of it. For instance, for penguins, there is already Delibird and the Piplup line - so maybe try another one. Depends however.
If it doesn't actually need made up Pokemon, I kinda question it, but it does depend on the fic and all. I don't mind it if it's done properly, and there are some good fics with them, that use them well. Also depends on how far you use them (if the fic focuses on them, or not). I'd also advise looking at fics with Fakemon done well just to see - doesn't hurt.