I'm talking the Nier Automata, the Dave the Diver, the... wait, that's all I got. Can we get a bigger list in here of games that defy or bend genre?

I'll add the most fitting to the OP. 

1. Sakuna of Rice and ruin

2. Cult of the lamb

3. Astebreed

4. Blast Corps

5. Cat Quest 3 (unreleased)

6. HifI Rush

7. The Plucky Squire (unreleased)

8. Minecraft

9. ActRaiser (SNES)

10. PalWorld

11. Metriod Prime (Gamecube/Wii) 

Thanks folks, this thread is gold. 

Nier Replicant counts too. Forgot about that.

Dave the Diver is a great pick.

Here are a few recommendations:

• Cult of the Lamb - part rogue-like action game, part colony management sim
• Sakuna: Of Rice and Ruin - part side-scrolling action game, part farming sim
• Creature in the Well - part hack-'n-slash, part pinball

Oh lovely, Sakuna is on PS catalogue and it looks really competent as a side scroller alone. Nice one. 

Total War comes to mind. A Grand Strategy series where it takes Turn-Based strategic gameplay on an overarching map, to resource management of a Real-Time Strategy game, then it dives into the map where your character is and turns into a Real-Time Tactics game where you're controlling hundreds/thousands of units on a battlefield.

This is all the overly simplified version too lol. I don't think there's anything like Total War.

Astebreed merges hack n slash with shmup and it's amazing.
Hi Fi rush merging DMC with Rythm games.
REZ. Merges Panzer Dragoon with music games.
Dungeon and Dragons Tower of Doom/Mystara/Dragon's Crown and Gaurdian Heroes merging beat 'em ups with Action RPGs.

Not sure if it fits, but I always thought pikmin was hard to pin down into a genre.

I disagree. Pikmin is a real time strategy game with puzzle elements. I think that descriptor fits well

VVVVVV is a semi-open-world platformer without jumping, where the hardest challenge in the game is getting over a knee-high ledge.

Has real time strategy for sure, but also adventure/exploration elements.  More so than Warcraft or Starcraft.  Especially Pikmin 4.  

Most RTS, at least the ones I've played, the player commands the units to fight and is a spectator.  Pikmin has full control over the battles with skill bring required, certainly with boss fights.  Always felt a bit action genre to me.

I do agree that Pikmin is RTS dominant but has a bunch of secondary genres tossed in.