I am thinking that I will not use flash to make an entire website. But I think that it would be good to use it to make small things like adverstisements, or photogalleries. I think everyone accepts flash and it seems to display the same in all browsers.
It also comes down to which technology you are most familiar with. If you are awesome with flash, I say go for it.
even with a dynamic content flash template, its still not as flexible as jquery. Remeber with jQuery you have complete control over your style options, so you can actually restyle and reuse your element quickly and easily.
But like Chris, im not anti-flash – it can look really sexy, especially for building moduals like you say, and not for full sites :)