Apparently before this stupid SMTxFE crossover, Intelligent Systems (the makers of Fire Emblem) went to GameFreak and all these other names associated with Pokemon to pitch a Fire EmblemxPokemon crossover, but the idea was turned down because at the time of the pitch back in 2010, they were already working on PKMN Conquest with another company. And while Atlus also originally refused, a year later, they returned to IS to see if the deal was already on the table. If Atlus had been just over a year slower in accepting, Conquest would have been released and thus the crossover might have been done with Pokemon instead of Shin Megami Tensei.
This is depressing, but given Tokyo Mirage Sessions #FE is now done and out of the way, I still have hope that perhaps we will see such a crossover in the future. I personally would love to see "Pokemon Emblem" so-to-speak.