Autotilegen still feels like it's stuck in beta and has some bugs - artifacts showing in areas that should be transparent as well as sometimes not sensing an image transparency (the beta was much better....). It will let you quickly produce a full tile set, however.
2D is more embryonic (no tile sheet export yet) but the interface is easier to use and the user can import their own masks and texture templates to make it very customisable. They even have a video showing how to import into C2 (using sprite, not tile map ). Shows more promise and is my personal favourite.... When tile sheet export comes it'll be a clear winner.
Edit - this should probably reside in Tools and Resources