This should probably go in the 'unpopular opinions' thread, lol, but two battle systems I kinda dislike are Persona 4 and Xenoblade.
With Persona 4, it's because the flow of battle is entirely based around weaknesses. You enter battle vs a new enemy, and immediately spam one of each spell on each different enemy. Once that works, just endlessly spam that spell, pile on, and heal when necessary. There was very, very little to it other than that. Add to that the awful dungeons (though I loved their 'themes') and you have a game that was really only great when you were in Inaba itself. (Though those parts made the game entirely worth playing.) The battle system wasn't awful, but it was pretty dull.
With Xenoblade, I loved the setup. The positioning of your character, the different arts (skills), the fact that each character was wildly different, and the chaining of skill buffs between characters using social links. The problem with Xenoblade was entirely in enemy design. They never advanced beyond 'get behind this guy and unload', or 'topple this enemy and unload'. The designers obviously knew this, so they threw in wrinkles like the Mechon who needed to be 'unlocked' for damage using the Monado first, or enemies that were only really affected by magic. But the vast majority of fights were the exact same thing over and over. Varying enemy design or AI would have made it incredible, but as it was it was a great system in search of actual gameplay to apply it to.
The same kind of applies to Pokemon. For the entire game you just spam your best move. The game never throws battles at you that make you use good movesets, so you don't even see the depth. If you get into battling with other people a lot, you see that it's an incredible system. Flawed (stealth rock and other such moves need to be removed post-haste) but brilliant. But the 80 hour main game does not use it in the slightest.
Two (edit: three!) that I loved:
Final Fantasy 12 - Others have covered this one. You loved it or you hated it. I loved it.
Golden Sun - As far as your classic RPG mechanics went, I thought this was as good as it got. The balance between using Djinn or keeping them as buffs was brilliant, and then storing them all up to summon... added to a phenomenal presentation and blistering battle pace - it was perfection.
Etrian Odyssey 2 - It was so perfectly balanced in every way. If your party wasn't set up well, you would get wiped by the easiest enemies. Making every fight interesting. Once you learned how to set up your party through trial and error and invested in good skills, you steadily became more and more proficient in the most satisfying way. It did not revolve in any way around any 'rock-paper-scissors' weakness mechanics, and both defence and offence were required at all times. It was essentially the 'Demon's Souls' of turn-based RPGs. A lot of SMT games are like this (thinking of Strange Journey here), but for me EO2 was the best.
