DS is a console port, PS3 timed exclusive, if I remember correctly. The game was designed for gamepads in mind, and you're wrong thinking input devices are not key components of games. They can be programmed to act as an invisible artifact for the player and his/her character, but that is not the only way to do this. From designing functions of buttons in a specific controller layout to programming the rumble motors, everything influences the way you play the game, and it reinforces the theme of the game, if done correctly.
Brothers, the game you missed the point of by playing it with kb+m, uses the controller to reinforce the theme of a bit weird nature of relationships between the two boys in a family. Later on it's more about the loss, obviously. Games like the DmC have great controller layout and character abilities that let you have this state of zen-flow, where you use functions and combos way faster than you think, in a super-fluid manner. It makes sense, because it reinforces the theme of being a supernatural asshole
In DS games the main theme is hardship. Of everything, really. You're a decomposing zombie, struggling not to get hollow in a world that doesn't give a shit about you. In the end, you're just a bit more powerful zombie, with the very same problem. The controls reinforce that theme, at the same time giving you the power to be whatever kind of zombie you want
And it's not that you can't control your character well, it's just quite hard. Look at youtube videos how people beat bosses or guys doing speedruns. They have mastered the controls. The very fact that this game is used for speedruns means it has consistent controls – how else would you shave off those minutes and seconds in subsequent runs, if the game mechanics wasn't consistent? Speedrunners wouldn't bother, there are tons of other games to play.
But you don't have to be that guy to understand that all this is by design. If the DS series won't teach you to question your approach, thinking more "I must be missing something" rather than "this game sucks!", then you are wasting your time. Like, looking for precise jumps over pits that you don't need to jump over, in the boss fight that ends with one hit.