Disclaimer: The most recent Final Fantasy game I have played is X (I think they’re up to, what, fourteen or something now?) so I am partially speaking from ignorance here.
Hmm. I’m not sure there’s anything that would help, particularly. Most of each game’s distinctive features have counterparts in the other that work differently but serve the same purpose. Materia, for instance, provides essentially the same gameplay function as TMs – offering a broad base of powers that can be used by most or all characters. Limit Breaks, as far as FF VII goes, give the individual characters their own special powers, which is something Pokémon already has quite a lot of. Their item systems work in essentially the same way, and so do their status effect systems – Final Fantasy has a lot more status effects than Pokémon does, but I’m not sure there’d be an particular benefit to bringing that over. I suppose one feature of Final Fantasy games I’ve always found interesting is the way the turn system works – not one-for-one, but based on a character’s speed, so very fast characters can potentially take more turns than slower ones as well as simply taking them first. It’s interesting, but shifting that across to Pokémon would be a balance nightmare – it’s not like speed isn’t already an important stat! As for going the other way… well, the same objections apply; Final Fantasy wouldn’t have much use for TMs, there’s no particular reason to simplify the way speed works in those games or reduce the number of different status effects, and Pokémon’s expansive and complicated type chart would sort of be a waste of time in a game with fewer than ten different player characters – Final Fantasy’s simpler elemental system makes a lot more sense for the needs of the game. I can’t really think of anything else…
It might be interesting to see the whole idea of Pokémon adapted to a Final Fantasy game, with a sort of ‘beast master’ type character who can tame and raise monsters to fight for the party. In terms of gameplay, though, a similar niche is already filled by Final Fantasy’s ‘Blue Mage’ character archetype, which can absorb and learn the techniques of the monsters it fights, so… eh.
