Well, first of all, 3 hours isn't really that far in, so a bit early to judge but hey.
First a few things.
On PC it is locked to 60fps, and the cutscenes to 30. Why? Fuck knows, but that's how they did it and not much you can do about that. Personally, while the 30 part sucks and I wish it all was 60, it is not enough to break the otherwise lovely experience I am having with the game.
While I understand your desire to play the game "the way it was meant", complaining about the control setup when it is one of the few games that allows you to reconfigure it to whatever you'd like seems a bit silly. Take advantage of that option and change it if it bothers you too much.
I for one love the standard setup, as it feels natural to me. It may be because I haven't played with a controller in ages and have no idea what "standard" setup should be, but it works for me.
As for the general style and graphics, it's weird as hell but I like it. Some areas are sorta boring yes, but others are quite stunning. The amusement park was really something special but wish it was longer.
Now let me give you my impressions, you didn't ask for it but I'll do it anyway.
I went into the game with no expectations at all, just wanted to try a new game I knew nothing about, and so far I god damn love it. Decided to go straight into hard, and even though I sorta regretted that decision after re-doing the whole intro part about 4-5 times, I stuck to it. It forced me to get good, much like in Dark Souls, and it gave me the same feeling of just being a beast once you start tearing stuff up. In fact, it has A LOT in common with the Souls games in terms of mechanics.
However, when playing on hard, the road from feeling invincible to getting absolutely recked is not long. Things hurt, and bosses straight up one-shots you.
I also love the whole skill system and the way they designed it to work, as there is tons of customization to be made there depending on how you play and what you are doing. It allows you to do silly stuff as well, like the idea I am playing with which is basically just going full on glass cannon. Thing's more or less one shots you anyway on hard, so why not just go on very hard, stack "perfect" damage up % in all slots, including slots meant for core systems, and then just go nuts.
If I have to fault it at something it has to be that it can get a bit too spammy at times. Like the sections where you have the flying suit, and as long as you just spam melee attack nothing can touch you. And not to mention the damn shooting thing you can do, where you are basically meant to just hold the button down constantly whenever you are in combat as there is no reason not to. After trying different things like taping it down or macroing it, I just said "fuck it!" and stopped using it, the damage it does isn't worth the hassle at the later stages anyways. Melee combat is a lot more fun, and without the constant shooting sound and the added visuals it's far easier to tell what the hell is going on as well.
The last thing I also wanna point out is the music, as it needs a mention too. It has been a long time since I've even noticed the music in a game, it's good. The track during the Opera boss fight is just epic, and the theme in Pascal's village is just so damn cute and lovely. In many ways it reminds me of the good old days playing Final Fantasy.
As for the story.. Well it's no masterpiece but it's good enough. It is different at least. As long as it keeps leading me from one awesome place with spectacular fights to the next, I don't really care though.