As soon as i joined Stencyl i saw what are his weakness, but i have pointed out all and now it's a better place.
I use Java applets too and i must say that Stencyl still gives you poor support with multidimensional lists, multiplayer applications,fake 3d and 3d, common components like scroll browsing, buttons, choice buttons and drop-down menu.It has also no support for objects and dynamic behaviour attachment,and that it eventually cripples your range of feasible programs.
However it's much easier to learn to use than Netbeans, it provides you the best working libraries around, you have all the preset objects you may want to use, you get a solid drag and drop system with a wide enough palette to make simple games out without doing syntax errors, you have an high quality code editor and no need to make glue code just to get pieces together.
I'd employ one week to get a prototype in Netbeans, while in Stencyl i'd get it in a day or two, with the same complexity.
gamesalad doesn't care if librairies actually work or are practical to use, and the beta is really buggy if you adventure out the tutorials' range.