Fakemon are not easy to use. However, there are a few things that I've learned about them that can make them work in certain fanfics.
1 - This is important. No matter what you do, no matter where the 'Fakemon' came from, do not ever, EVER make it Legendary, if the protagonist is going to get it. If you're going to use it as a Legendary, make sure it's not something that the main character catches. This is a big turnoff, and honestly one of the most predictable and cliche plot points in alot of fanfics. Making this mistake can very easily turn an otherwise good character into a Mary Sue/Gary Stu.
2 - If you're going to use Fakemon, don't use too many of them. You can use three or four, maybe five (though that could be pushing it, if they're all used frequently), but I would not recommend making an entire 'Generation' out of them. This is what I call the Fakemon Confusion Trap. You've got a fanfic that introduces over 100 new Fakemon, and now the reader is struggling to keep up with what each of them looks like, and what each of them can do. It becomes a problem, and can make a reader lose interest very fast. So the solution is to avoid it by limiting the number of Fakemon in the Fic. Focus on the few that you really want to focus on, and don't use any others.
3 - Make sure you DESCRIBE the Fakemon, to the point where the reader could draw a picture of it the way you imagine it to look. Ok, that's a bit of an exaggeration. But the point here is, very few Fakemon get enough description to make them stick in the reader's minds. If you're creating a fan Pokemon, then evidently you personally know what you want it to look like. So describing it in detail, including how it looks when it attacks and does other things, should be one of the first things you think of before even using it in a story.
A Winner Is You!!!
If you spend too much time thinking about a thing, you'll never get it done.
- Bruce Lee