I finished the game recently and I agree with everything you said. The game was a frustrating mess at many times, boss battles in particular were often terrible. All the weird minigames were crap and annoying to control, except for one which I wont spoil. The Gamepad sections were absolute trash, each and every single one of them. I found the level design to be lacking too, especially the chase sequences. Platforming was poor, like you said. The plot also started to grate on me aswell.
But somehow I still ended up enjoying the game enough to finish it. And honestly, all the frustration was worth it to see the final battle. It's seriously one of the greatest I've ever played in a videogame.
Alright, considering you seem to think the same way as me and liked the ending I guess I'll finish it.
I didn't even mention the terrible gamepad sequences or various bugs. The worst bug for me was the hydra battle in what I think is the first chapter. You have to fill its eye with dudes and no matter how many you cram in there nothing happens. Had to reset twice before it would work, tried it about 12 times each. Quite a few little annoying things like that in the game.