I use a lot of flash, but _only_ for illustrations that require it. Generally, it's just a pain on an opening page. While Macromedia (now Adobe, Inc.) will tell you that Flash is the most common plug-in in the world, and some huge number of people have it, it does not mean they LIKE it.

You can do a lot with javascript that might be easier with Flash; my humble opinion: spend the effort to script rather than Flash, and keep it simple.