I don't like it. It's not just the glasses, although yes, I am not a fan (even before I got glasses!)
I don't have a lot of technical detail for my feeling, but I feel like 3D doesn't suit most movies. Avatar was filmed for 3D and directed to look beautiful and natural that way, instead of having it tacked on. The only other movie I've really liked in 3D was Coraline. For stop-motion, 'natural' isn't really a concern!
I often fail to discuss this preference with my friends when they're the ones choosing showtimes, but luckily it seems to be general (perhaps not surprising, since one of my movie buddies is legally blind in one eye!)