Who gives a shit? Some people will make the shift to new programs, while others won't. People still make decent art in MSPaint. Of course some people won't make the change because they're scared of leaving their comfort zone, but if you're a good artist it shouldn't matter, and you should've been relying on your own skills rather than what the program can do for you. I can't really say what's better for programmers, but I think it's fair to say that being able to adapt is an important step. I imagine this could have a major change on commercial games, but independent artists will continue to use whatever they're comfortable with.
In the end the software doesn't make you what you are. And if it does, well, sucks to be you. If tomorrow Flash and After Effects disappeared and were replaced with a new program that could only do frame-by-frame animation, Sam T would kill himself.
Intrapath
I played a few games on the site, and I must say I'm impressed. However, I don't think the game you linked to was the best example, that game was pretty close to what flash can do. You should've linked to Time Donkey, it's much more awe-inspiring. I still don't think flash has much to worry about though, it'll adapt with time... :P