There would be two kinds of fusions.
Permanent fusions would only work for NFEs and single-stages with low BST (ex: Pikablu), so they end up as just regular pokémon with a different evolution method.
Temporary fusions would be like megas (ex: Lucarizard), and balanced by the fact that you're using two pokémon in your party as one.
In both cases, only about 30 combinations would be available at first, and less than 100 before GF moves on to the next gimmick.