There are two things I don't like about the Joy-cons;
1. They're too bloody small! I mean, I'd say I've got small to average hands but playing with just one Joy-con is actually dreadful for me and I start getting a horrible pain in my thumbs after about an hour or so of playing.
2. The fact that, when separate, the Joy-cons aren't identical/symmetrical. One of them has the buttons in the middle and analogue stick on the right, the other has the buttons on the left and analogue stick in the middle, it drives my OCD insane and whenever I'm playing a two player game I literally have to sit and decide which thumb I'm okay with aching like fuck because of the positioning of the controls.
Aside from those two things though, I have nothing to complain about.