Well, sure, and Nintendo really could have used GTA on the Gamecube instead of the PS2 back in the day. There are some obvious upsides to relying on third party support, but one of the downsides is that you can't reliably predict which game is going to blow up and be the next huge hit. It's obvious in retrospect, but while it's happening, it's not. In its first week, Youkai Watch was just another game selling ~53k.
Why do we expect the next Mario, DQ or FF game to do well? Because the previous ones did well.
Why do we expect the next media mix franchise by L5 to do well? Because the last one did well.
It was perfectly clear even before it launched that YW would follow the I11 pattern. First week was actually in line with that. The anime was already known to hit later, it was perfectly expected to do well. YW just managed to further build on I11's success, suggesting that L5 brand strength has risen as well.
Another factor would be that it is on the same platform as Pokémon. YW launched before Pokemon released, the anime and the sequel after it.
Even if Sony had courted L5 for YW though, like they're doing with all the mid range hunting game franchises, it wouldn't change the fact that the Vita doesn't appeal to kids.