With Fakemon, one has to be careful. You have to be able to describe them well enough so that the readers can see them in their heads. That could be difficult to do if you don't want to sound like a text book on your Fakemon. The readers have never seen these creatures of yours before, and they might have a somewhat tough time picturing them.
The other problem might be that some readers will see your Fakemon and wonder why you couldn't just use the canon Pokemon. Unless your Fakemon fits into a role that any of the 493 Pokemon can fit into, you might be better off using one of the "known" ones. Of course, I can't really say without knowing anyone of your Fakemon.
I still say to try out your fic. See how things go. There's no accounting for everyone's tastes, and there are those who enjoy a Fakemon fic just to see something different. And to me, difference is a good thing.