JMich: I know that the gamepad recognition had errors if using anything but a proper 360 controller, but I thought that was the case only with the wireless ones. The fact that this is not the case is interesting though. Will probably have to reinstall and verify it, hopefully later this week.
I've been under the impression that the Logitech F310 in XInput mode works identically with the genuine XBox360 PC gamepad with any game you throw at it. For instance Darksiders, which was claimed to be a "works only with the genuine XBox360 wired gamepad, period" works perfectly with the F310 (XInput mode). I felt those complaints were related to people trying to use their legacy DirectInput gamepads with XInput games, which is certainly iffy in many cases.
But if it really is true that wired XBox360 controller works perfectly with AssCreed PC with default settings and without any additional software (while F310 seems to have some issues specifically in XInput mode (but DirectInput mode works perfectly)), maybe it isn't quite so then? Dang, I want to test it out to get some hard facts and not just assume. Maybe I'll buy a XBox360 wired controller. It never hurts to have a backup gamepad (albeit I'd actually still prefer to buy a second F310 instead :); I won't buy a wireless F710 until Logitech makes one with Unifying support, so that I can use the same wireless USB receiver for it which I am already using for Logitech wireless mice, keyboards and trackballs).
Either way though, at least for me F310 seems to work perfectly with AssCreed in DirectInput mode, without any fiddling. All the controls work (including both analog sticks, the D-pad and triggers), all the controls seem to be mapped into logical places, the color coded buttons are mapped correctly etc. Plug'n'play.
One possible explanation would be that AssCreed still recognizes F310 as a "non-XBox360 gamepad" even in XInput mode, hence offering only DirectInput support for it by default. Ie. like you said, the game would support both DirectInput and XInput for gamepads. It would be the first, I think games usually support only one of them, not both.