The more I think about this from a mechanical standpoint, the more it seems like a good idea. Again, limit it to 50 fusions... Make them alternate formes, listed under the same number as their first component Pokemon... Name them accordingly... And prioritize Pokemon where it would seem redundant to give them proper evolutions. For example, why give evolutions to both Plusle and Minun? It would be simpler to give them one shared fusion. Same for Pachirisu and Emolga -- fuse them into one flying squirrel (they're both squirrels, anyway), make it a strong Electric/Flying-type, and call it "Pachirisu [E-Pachirisu Forme]." It's a way to power up twice as many Pokemon with half as many new formes, and it could make for some fun designs. I don't see how this would be problematic. Again, it would be done in a smart and balanced way, essentially as an evolution alternative that gives greater potential to similar species (or dissimilar, as the case may be) that otherwise likely wouldn't receive an evolution.