The difference is, right now, that the 3DS doesn't just have more games, it has games in more genres. It has the cute sims that appeal to females, the collecting games that appeal to children, and the big franchises that appeal to older demographics. That shows the focus of Nintendo in the handheld space and the focus of Sony in the home console space. In that regard, it's understandable and expected that Sony's handhelds should have a lower market share.
There is a definite niche for the Vita, though, and it's the same one the PSP still holds as the otaku system of choice. Personally, I think the Vita will be fine, especially now that developers are seeing that it can have strong software sales even with a small installed base. It only makes sense to dive into a market that is wide open. If developers and publishers had doubts, I think those doubts are being exorcised.
