I think you're absolutely right, Beelzebufo. There are plenty of little touches you didn't see in games back then--I'll keep this pretty spoiler-free--destroyable checkpoints, Digger's Diary, and a level with lightning flashes affecting platforming, to name just a few.
Let me address a few of these:
-While destroyable checkpoints are a novel idea, I think the execution is sort of bad. The checkpoints themselves are so plentiful and populating stages that are easy (this ramps up later in the game admittedly) that they may as well not even be there. If you play with checkpoints, I'd imagine the game almost has zero challenge. I feel a traditional checkpoint system (beginning stage, mid stage, boss) would have honestly worked better, even forcing players that rely on checkpoints to learn the stages/patterns to progress, but I do appreciate trying something new.
-Digger's Diary is a nice borrowed idea from the Souls games but I wouldn't know about its implementation as I played it on 3ds
-Lightning (dark to light) platforming has actually been done in NES games before.