1. There are a million small disadvantages to using proprietary plugins, it is not "the internet", google can read flash, but not well, you dont have firebug, your site cannot be scraped, these may not all affect you, but there are lots lots more.

2. The flash plugin sucks on most browsers, its a slow unreactive user experience, compare a few full flash sites to their equivalent in javascript.

3. Flex's layout constructs are similiar to pretty much every widget manager around, are in no way close to the power of xhtml/css, I for one didnt find it enjoyable at all to develop for.

how long have you been doing html/css? its a pain that goes away quite quickly, if it hasnt, I would ask some more experienced developers to look over your stuff and see if anythings being done wrong.

and you might want to look at graceful degredation, if ie isnt a particularly large chunk of visitors, your exact problems are very easily solved in a way that very gracefully degrades (-moz-border-radius:, font-face:)