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We are talking about a company lazy enough that they made their models sub-optimal for the 3DS so that they could reuse them in future games. No way we get full-blown fusion on a wide scale. But full will happen eventually at some scale. We will probably get a bunch more Kyurem style legit fusions for popular mons as the next HYPE feature after megas lose their marketing punch.
But for the rest, I think a more feasible mechanic that won't require tons of effort from GF's part is the idea of inheriting color pallets. For example: a Skitty with a Wailord coloration. Some sort of procedurally generated program that changes a mon's coloration depending on the parentage or something like that would be easy to pull off and create endless combos. GF could even release event exclusive colorations for legends or other mons that are genderless.