we use netbeans, so i don't have code assist. To be honest, I think it has made (forced) me to learn the API more thoroughly.
You loose a lot of handholding/drag and drop/gui/styling etc.. by not using Flex. But you gain control and security. Totally worth it to me.
As far as the jquery/dojo thing, i found myself recently forcing jquery OUT of my code and doing everything in dojo. Think I am better off for that as well, but i don't know jquery very well either. I have yet to find something dojo could not do.
Finally,
We still support IE7. I recently had to wedge client side pdf rendering and printing into ie7 without canvas elements. I ended up using flashcanvas instead of excanvas due to image support. If we ever get to full html5/js I will be a much happier camper.