I find it difficult to comfortably hold the 3DS too. Before buying this the only DS I had was the old one, and while it was a little clunky looking, I found it much more comfortable.
I notice that when playing my left index finger now automatically goes up to the top screen to "brace" the device otherwise the weight/balance feels completely off.
This also helps keep the screen from "wobbling" but sometimes when the playing gets a little too intense I will press too hard and the top screen snaps back into the furthest position.
Anyway, the overall design is pretty annoying, but even though I haven't played a DSL or DSi, I imagine those are similar. Sadly, I am guessing this new "cradle" device with the extra analog stick, etc. is going to make it MUCH more comfortable to hold. Although I don't want to be carryign that around...
Nintendo should have designed it in a shape more similar to the PSP or Vita instead of the weird square design but who knows how well that would work with the flip-up dual screens. I guess dual-screen is probably inherently hard to design well.
I am thinking of getting rid of the 3DS and getting a DSi XL because I currently ONLY play DS/DSi games on it. I just wonder if all of these new DSiware games would transfer from 3DS to DSi XL. I highly doubt they will even though the other way around is possible.