The 3DS is a really flawed piece of hardware, it really needs a new iteration.
What flaws really? It's a perfect size, really comfortable (unless you have gigantic hands), the stylus spot is fine. The only hardware flaw is the short battery life (I know I have seen people complain about the screen leaving a mark, though this hasn't happened to me)..
In addition to the two you mentioned:
- The start and select buttons are pretty bad, especially if you play a GB/NES VC game that assumes start or select is easy to press.
- The load times are really bad even in the OS, it takes a long time to load the main menu, then a long time to open the options screen, etc.
- The circle pad pro isn't integrated.
- No way to change the brightness without going to the home screen which doesn't work well with ambassador games (DSi allows select + volume switch to change that)
- Terrible rescaling for DS games
and I think I had some other issues with it but I don't remember them.