While I'm not one to decide, porting something to another framework is never a trivial task. Flash AS3 comes with a lot of useful functions from the main framework and has loads of useful libraries available to help achieve your goal faster. Of course libraries exist for Qt, Haxe and Mono too, but nothing is 100% alike, which means more headache and less "fun". About the "clean" you speak of, it has no real use to me as the source is not available to us. If Danik feels home in AS3, then by all means he should just write in that language, no matter how obscure its syntax is.
Given that it already takes a fair amount of time for each release of PE, I would be against any kind of porting, even if for the better. Porting is in my opinion the most boring kind of task you could give a programmer because it requires you to rewrite your work from the bottom in another language for the purpose of trying to broaden your audience. If you are already tired of a project or simply do not have enough time to even update what you already have, then porting it to something else is often the last kick you need to quit entirely.
Should Danik ever consider porting PE though, then I hope he does it when PyxelEdit is feature complete.