Different locales, characters, gameplay mechanics like marking for Splinter Cell Conviction-esque instant kills mid-battle and switching into disguises to manage notoriety or just go about missions in different ways (eg, the last mission I completed by charming guards and luring them behind buildings before stabbing them repeatedly. Very satisfying. I could have also just gone in wearing my Assassin garb guns blazin').
It's also not really about the American Revolution. That's the setting, but it isn't the focal point of the story like it is in AC3, where you're constantly getting involved with Franklin and Sam Adams and the like. ACL's story is more about Aveline than anything else, at least after the first few sequences. And she's a freaking great character in my awesome opinion.
Basically, it's a different AC game entirely, just set around the same time period. And since the game doesn't really lend itself to short, 5 minute sessions here and there, I don't really need it on a handheld. It's not that I prefer ACL over AC3, just more that I'd prefer if I could play ACL the way I play AC3; On my bigass teevee, hours at a time.