Yes. The stand by function of the Vita is more taxing on the battery than the 3DS's sleep function mainly due to all the background syncing it has to do with your friends, messages, trophies and the like. It doesn't last as long as the 3DS unfortunately.
I found the Vita's stand-by works incredibly well for conserving battery life, though I put it on flight mode unless I want to sync trophies, saves, or just download stuff. It probably doesn't match up with the 3DS in sleep mode, but even that goes down by a bar during a long day for me.
As for this game, I'll have to see how they plan on forcing us to buy two editions AND if they plan on DLC (haha). The one annoying thing about the Vita is managing regional accounts on one console, so I'd probably have to switch to my Japanese account for both games in the end.