Yeah, generally, I think cross-overs should be either "fit like a glove" or "ah, what the hell".
Hyrule Warriors is a "fit like a glove" crossover. Aside from the puzzle aspect of the series basically just being thrown in there, there's really nothing special going on here; just fan service. And that's fine,
With SMT, the only thing that interests me, from a Fire Emblem standpoint, is the possibility of a modern setting, from a storytelling standpoint. Aside from that, I don't see a lot of benefit from either series for each other. Rather go with something with either more contrast or something more like it. "Fire Emblem Warriors" for instance would be boring, but great fan service for either fan of the opposing series, especially since Fire Emblem is traditionally turn-based.
Edit - FIRE EMBLEM BATTLETOADS