It seems like practically every developer I see is working in Unity, a 3D development tool that just recently added better support for 2D games. I wanted to learn Unity partly to allow me to work with other Unity devs, but also because it opens the possibility of using 3D at some point. The UI isn't something you can just pick up and use since 3D games are generally more complex than 2D games, but their video tutorials help a lot.
Unity does a good job with modular code reuse, which is the thing I like most about Stencyl. While Stencyl's click-together code blocks are also nice because they make it impossible to make syntax errors, that gets pretty hard on your mouse-wielding hand if you're going for long development stretches. I found it refreshing to bang out C# scripts in Unity. These scripts can be assigned to any game object, allowing the designer to tweak script-specific variables in the Inspector window (just like "behaviors" in Stencyl). The combination of visual mouse-based editing and basic coding in Unity is appealing, especially with the vast body of pre-written modules for you to use.
I've been hesitant to try working in 3D because of how intensive modeling and animation is. Some developers have implemented a low-poly art style that makes this less of a problem, which is akin to using pixel art in the age of HD graphics. I see this especially in 3D games that come out of 48-hour game jams.