It does require separation of code, but not twice as much debugging. Every bug does not have to be fixed twice. It's similar to MVC architecture in a way, with the flex client being the view. I'd be surprised if the bug fixing isn't actually easier due to the separation.

Also, your goal in a startup is not to make it easy for you to code, but to make it easy for your users to play. (You only do the former where it assists with the latter.) Java does not accomplish that. People don't want to piss with JRE. It is a bloated nightmare that crashes people's systems, nags them about updates, slows down bootup, etc.

Everyone has Flash. In fact, more people have flash than javascript (turned on) making it the most commonly accepted environment. It and AJAX are really the only acceptable choices for a live draft.