No, Arkham stayed with Eidos through its whole development, being handed over was a post-release event (and not until sometime after Square Enix started labeled Eidos games as Square Enix), and checking quickly the development team was bigger: Stick of Truth was at 50, and Arkham Asylum 60 if the South Park Wikia and Wikipedia respectively are to be believed, neither all that big compared to some games actually. And review wise we're talking about a game that was getting piles of 9s and ultimately averaged at 91 on each platform if I'm remembering right, whereas we've only just begun to see Stick of Truth reviews.
Which is the best is down to opinion, yeah, and it may well be on track to be if not the highest rated then at least standing roughly toe to toe with the likes of Arkham Asylum, but like I said the initial statement was really, really easy to rip into.
... then there's the Riddick game, but something's kind of messed up if more people knew about the game first than the original IP.
