I have the same issues here that I did with PoR. That is, the game mechanics aren't very well integrated into the level design. For example, when Shanoa walked into the Magnes Glyph room, I knew instantly that those awkward out-of-place bars were meant to be used as such. Instead of having something that's integrated into the background serve the same function (statues, crumbling walls/columns, etc).
Also, not once since SotN has the platforming made sense. Since when do monasteries contain large vertical shafts with absolutely no stairs and floors jutting out of the walls? I know, it happened in SotN, however, not nearly as much. The backgrounds in SotN had stairs that indicated the area could be used by people that aren't able to fly ten feet into the air. The problem I have with PoR and now OoE is that the areas are built around the main character, with little concern as to how normal people would, in theory, interact with these areas. Yes, it's a monastery, but it can't be used as such since the rooms are separated by long vertical shafts. How would a priest, for example, be able to get to the top floor?
Anyway, that's just my opinion. Please feel free to disagree.