It is a bit of a pain to take several hours to convert a working codebase in one language/platform to another. I kept having small problems with JRuby and Sinatra that were just AppEngine specific (Ruby (or JRuby) and Sinatra are awesome).
I am only about 20% into development, and I decided that I wanted really solid tools/platform. Also, converting working code in one language to another is simple.
What convinced me to make the switch is that Java + Eclipse plugins support is just so good for AppEngine development, that for now the change seems like a good decision. For my next AppEngine project, I'll probably go back to JRuby + Sinatra since the support is getting better.