Wait for the refresh
I got my 3DS a day early thanks to Play.com sending stuff out too soon, so I've had a few days with mine and I think in a year or so we'll be seeing a refreshed model, just like the DS Lite fixed all the problems of the original DS.
The 3D screen is quite dull, even with 3D off, especially so in daylight. I could easily see a new model with a brighter screen turning up. Maybe my eyes are too close/far apart but the sweetspot for the 3D is quite narrow and sometimes I find my eyes lose focus during a game (Ridge Racer mostly) even though I don't think I've moved the screen. It's almost like the screen is ghosting or each half of the image occasionally goes out of sync. So a bigger, brighter screen with a better viewing angle would certainly be welcome.
Then there's the ZX-81 Start/Select/Home buttons. Not only are they almost totally flat and therefore not easy to find by feel alone, they are also quite difficult to press and make pausing a game quite a pain. I keep reaching for the power button instead of the pause button because it sticks out and is roughly positioned where the start button usually is. Thankfully so far I've not killed a game halfway through!
It would be nice if they could move all the LEDs inside the lid. I had it on the bed next to me last night and I had two LEDs constantly on and a third blinking at me all night. Does it need these all the time?
The games I've got are good fun (SSFIV3D, Ridge Racer 3D, Pilotwings Resort), and the hardware is mostly there, but my main nagging concern is how the 3D can actually be used to make unique games. At the moment, I don't think it can, especially since there's a slider to turn the 3D off. The DS created unique games thanks to having two screens and a touch screen and the Wii was unique with its motion and pointer controls. The 3DS doesn't appear to offer the ability to create unique gameplay experiences with what it has on board, and I think that could limit its long term appeal.
All that said, I thought the DS was a dud at launch and look how it succeeded. Only time (and the games) will tell.