I can't wait to play Phoenix Wright on my Vita.
They'd make less money. That's pretty much it. They make quite a bit from licencing, as well as lots from their IPs like all the Pokemon tat, plus of course a bigger cut on the games themselves.
I am probably going to get shot down in flames for this, but is there any reason why Nintendo wouldn't just be better off making software only with a peripheral to stick in another console?
Also don't forget some of the hardware that makes the Gamepad so low latency is in the console itself, so I'm not entirely sure it's be feasible to have it as a peripheral only. Might be possible, I'm not sure.