I see where your coming from. But software is irrelevant when deciding the "best" portable console. From a design point the Vita is near flawless.
It also has a better software lineup for me personally than the 3DS. It just doesn't have the big flagship titles to draw a larger audience and Sony have severely failed to demonstrate just how good their system is.
I do have a 3DS too but that's just for Nintendo games.
I'd have to say if you were going to bring software libraries into it, the original GB/GBC/GBA lineup is still the one to beat.