-The 3D mechanic will force obsessive compulsive secret hunters to play as the most boring character.
This is me. I'm the type that switches to Goombario/Goombella every time I enter a new room and tattle every NPC with them to see everything I can, and it's that very instinct that actually led to me missing the majority of interesting dialogue in SPM because I always had to play as the mute character because he can flip and there might be something to see in 3D.
open the menu, equip/unequip the boots, and close it. Having to repeatedly change your focus like that is grating.
Relatedly, it's a bit more minor of a complaint, but the hub world is annoying to navigate, since the 2D-only layout meant it had to be divided into multiple floors, and switching between floors takes longer than it really should. In Rogueport, I could really get a feel for the different parts of town and remember where everything is pretty easily over time (and it didn't take very long to navigate around the town anyway), but I have no idea where anything in Flipside and Flopside is.