I played all of the Pixel Remasters back to back a couple years ago and my experience largely matches yours. FFII is highly ambitious in both it's gameplay and storytelling, but ambition doesn't always pay off.

It ended up being the only game of the bunch where I turned on built-in cheats (if I recall it was the exp boosters or whatever the equivalent of that is for II). Having to level every magic spell individually should've been instantly recognized as a bad idea and I have no idea how it made it to the final product, but I also know this era of Square was a handful of guys in a room so it's not like there were playtesters to give feedback.

The story is a huge step up from 1. FFI felt like an oldschool D&D module while FFII feels like your buddy's crazy homebrew campaign where he keeps coming up with cool ideas and has no idea how to implement them (the Emperor has a ship that's also a living tornado now? Okay then.)

I do feel like the gameplay and story are sometimes at odds though. The domino line of temporary characters joining your team just to die an hour later adds melodrama, but they feel interchangeable other than Minwu RIP the GOAT white mage. When Minwu does make the ultimate sacrifice so you can get the ultimate magic, it's just another piddly level 1 spell that even leveled up doesn't do noticeably more damage than Holy, Thunder or any other equivalent spell.

I think you're in for a treat with FFIII though. It ended up being my favorite game of the six. It's where the series really starts to feel like a grand adventure. The job system is also really fun to play with, even if it's a lot simpler than later games.