The nickname issue would only bother me if I received one in a trade that had a really ridiculous or offensive one. Has yet to happen, thankfully.
The only thing that really bothers me is the disobedience issue. I find myself wanting to start over with a team I've never tried before (get bored with the early Pokemon fairly quickly), but with the day care several hours of gameplay away (so I can't start with freshly hatched Pokemon) and the fact that traded Pokemon won't listen after a certain point, it's just too much of an irritation to think about. Wouldn't be such a big deal if there was more variety early on, but what are you gonna do?