Search for Assassin's Creed 3 on the Uplay store and you'll only see the new remaster. The same is true on Steam but the original version's store page still exists. However, the purchase button has been removed and this text has been added: "Notice: At the request of the publisher, Assassin’s Creed® III is no longer available for sale on Steam." If you already own the game on either service you should still be able to download and play it. (I tested it on Uplay today and it worked fine.)
The same thing has happened with several other remastered games, like Sleeping Dogs for instance. While it's a shame players no longer have the option to save $10 or so by getting the cheaper version, and it's also a shame to lose the historical value of being able to compare both versions, you can see why a publisher wouldn't want players to be confused or accidentally buy the wrong one.
As well as graphical changes, the remastered version features free-aim archery, an improved minimap, more stealth options, double silent assassinations, and apparently the early ship section has been shortened.