I wish I could be more specific, I realise the complaints are super-vague.
Playing this game feels like watching a movie that's coming in and out of focus at random intervals, or something. I can, for all intents and purposes, kind of work out what's going on and what they're trying to do, but for the most part I'm still very aware that I'm sitting in a theater watching a movie because I'm being CONSTANTLY reminded that I'm watching film on the screen that was shot with cameras, rather than being immersed in the story and the presentation.
This game is filled with stuff that trigger this reaction. The controls, the way you have to hold the system, turning on the 3D when you're holding the system (maintaining a completely straight-screen all the time when using the stylus/left-hand setup seems near impossible to me, but maybe I'm just "doing it wrong"), mapping the stylus pointer to a thinner bottom screen than the wider top screen and putting stuff on the bottom screen when they know damn well the game is so fast paced you're never going to look down there (else your hand/stylus is covering it) all take me out of the experience of playing the game.
I have some other complaints, specifically about how it seems there are some weapon types that seem broken against certain enemies, but that might just be my lack of experience. I've only played through chapter five.
I also think the overall art direction and enemy design is a little too scatter-shot. I don't latch onto anything because it all feels so tonally mismatched when put next to one another, each world might as well just be a series of colorful hallways. this complaint, again, is kind of vague and may be the result of only having played a few levels.
It's so completely different than anything else I've played recently. I really want to like games that try to be something out of the ordinary. It feels ballsy and fresh and it slaps you in the face with a clear "fuck you!" authorial intent/vision (major point of endearment for me regarding anything, see something like God Hand). But it seems to me that the net result of all of these things is ultimately a negative thanks to a complete disregard for practicality of control.
I don't know, maybe I'm rambling and still being super vague, but the tldr of it is that I should like this game, and it genuinely disappoints me that I don't. I haven't been this disappointed in a game in a while.