I'd first like to say that I understand that these are two very different series, despite the fact that they both include 'monster collecting'.
However, I've seen quite a few people try to argue that Pokemon has a deeper combat system than SMT (mainly 3, 4, and 4A). Now, I'm not exactly the biggest Pokemon expert, as I've only played black, but my biggest issue with the game was the simplicity of its combat, given the 1 party member at a time limitation, the only 4 skills per pokemon thing, the uselessness of buffs and debuffs, etc. And this was before I even started playing SMT games, which honestly changed the way I see videogame combat. So I really cannot understand how someone could think that Pokemon's combat has more depth.
One of the main arguments I've seen is pokemon's IV and EV systems, but from what I understand all they do is affect a pokemon's stats. SMT, on the other hand has you managing your turns with the press turn system, usefull if not crucial buffs/debuffs, 4 member parties, fusion with changing results depending on the demons' race/stats/abilities, and much more.
Again I'm not a Pokemon expert by any means, and I'm aware that there are probably other mechanics I don't know about, but I really don't see how Pokemon's obscure mechanics can compete with the variety and complexity that current Shin megami tensei games have.