But the main reason I've stuck with it is that Babylon has a compact, active set of devs (I've made bug reports and seen the fix in the next nightly build multiple times). So it's been really easy to get help and get bugs fixed. Three has way more people working on/with it, but the flip side of that is that it's way harder to find help, unless you know a good forum where some experts hang out, or similar.
The other big difference is that Babylon is more of a "game engine" than a "3D engine" - it has built-in subsystems for stuff like bone animations, audio triggers, etc. I imagine Three has similar stuff, but I believe they'd be plugins or modules that you'd need to manage separately. I don't actually use any of these Babylon subsystems though, so I can't say if they're useful or not.