Look at how bad AC plays on Vita and ask yourself, who would buy AC on the 3DS?
Ubisoft shipped 600k of ACL because it was bundled and Sony basically gave it for free. Let's not play dumb, nobody is checking for that turd.
Iwata likes to play dirty though, and a few months ago he mentioned the ACL crazy bundle and deals, so maybe he's planning to do the same this holiday season.
EDIT: Looking at Takao's post, the source seems legit, I have also heard of RL on Vita, and as some people have mentioned before, it's probably being kept under wraps because it's a $40 game versus $60 on consoles.