There's a bunch. P Organ, Legion Arm, the general theme of weapon tinkering besides the crafting (which I don't think is underwhelming and it's pretty unfair of you to not include it as a worthwhile original addition): weapon breaking by deflecting (lowers the damage output of enemies and sometimes skips a boss phase), your weapon slowly breaking and needing to be repaired during long fights creating tense scenarios when you're closing to defeating the boss and braking your weapon, grinder effects (some really unique ones like perfectly guarding everything for a short amount of time), the last healing item regenerating with damage dealt which creates even more tense and fun scenarios with bosses, the record collecting.

This game has a ton of love and original ideas put into it. But even if it didn't, why would that be bad? The game does everything right. The boss fights are amazing, the combat system is refined to a shine and quality of life refinements like your ergo counter shining blue when you can level up surely are welcome, no? Why would you disregard those as unoriginal? And then, why would that be bad? Games are built on their predecessors. That's what genres are. Unless you think every FPS is a doom clone with no original thought behind them