If you don't do it now you will never get another shot at it, interactive elements and Easter eggs that lead to secret things once there gone there gone forever!
Browsers are also adding other components that could run flash.
You can even run certain versions of Microsoft Windows in browser with WebAssembly/javascript.
The flash plugin is just an app with Browser specific features Thus we can have a means of playing flash without having to install a plugin.
Proof its possible
https://www.google.com/search?q=Windows+98+in+web+asm
Future browsers will be perfectly capable of using Dosbox to play DOOM its not a big stretch to get flash working in such a way, we could even streamline it so new grounds would work the same as it always did even if there is no flash plugin!
our biggest concern is how newgrounds needs to get its audience back right now, i did a news post about this, maybe other people could throw around ideas
HerbieG
Take a look at it from the other side: it makes those interactive battles elite :-)
Maybe try to do the opposite? Make a game with such battles, rpg-style evolution, upgrade system with some cut-scenes? With your skills I'm sure it would be of very high quality, although I know that it would require some time.
teejay-number13 (Updated )
A full blown Pokemon game wouldn't be practical in flash. Besides, the story takes precedence over the battles.