Sweeny Todd was based on a popular Broadway play with Burton and Depp in which the former was coming off three consecutive financially successful movies (Big Fish, Charlie and The Chocolate Factory, and Corpse Bride) and the Conjuring only cost $20 million to make so there wasn't much risk there.
Sleepy Hollow I admit you could go either way on. It was a $100+ budgeted Rated R movie that was a success, but it was originally supposed to be a $30 million movie until Burton came on and suggested they build a town for Sleepy Hollow after failing to find a suitable actual location for the movie. Burton may not have been as hot at the time, but he was still known as the guy who made Batman and was supposed to be make a Superman movie in the 90s.
The problem with Del Toro is that while he is a great director, he's still not a proven box office entity in Hollywood. Pacific Rim did well overseas, but it bombed in the US, and while HellBoy 2 did good numbers, it got overshadowed by a few other movies that got released that same Summer, most notably Iron Man and The Dark Knight.
I'd like to see the movie happening, but in this case, I understand where Universal is coming from in terms of pulling the plug on this movie. It was too much of a risk for them at the time.