Controlling Mario in the water?

yes it is indeed a bit convaluted to control Mario in the water sometimes! My suggestion is to take it slow first, get to mind your aquatic surroundings and don't rush your swimming all the time! Once you can handle a steady swimming pace, you will be ready to tackle the swimming challenges available in the game quite delicately! There isn't anything wrong with the swimming mechanics of the game, you just need to practice just like all the other skills in the game! Take it slow and steady, then build up your momentum as you get more used to it!

Yes it is really hard, especially when you have to go deeper or rise up and the camera angles don't help much either. Grab a turtle shell, that makes it a tad easier.

It's not so bad. It's a bit easier to control if you grab a shell though.