I'm going to be unoriginal and also mention FF's job system, particularly the examples from FFT, Bravely Default, and X-2. Essentially, any Final Fantasy game that features jobs I will find more exciting and engaging than those that don't (weird that I love IV and VI so much, though I guess their biggest strength is that you can just jump in and play).

I adore Vagrant Story, so, once again I'm going to name drop it. That being said, I forgot how much I LOVE customizing Aya's weapon load out in the original Parasite Eve. Shooting poisonous grenades out of a sniper rifle is a thing you can do; that's equal parts ridiculous and magical.

I always enjoyed the Crest Graph system from the PS1 Wild ARMs entries. Being able to reassign what spells Cecelia/Lilka learned was always appreciated. Even more than that, I liked how each character in the original had their own method of progression. Paying to upgrade Rudy's Arms and discovering new techs for Jack in the wild gave each character a distinct personality with regards to how they grew.

I was going to type how I liked Chrono Cross's element system in theory​, but I feel like that's better suited to the Battle Systems thread.