I've been using both FlexBuilder and FlashDevelop at work lately. I'm a long time FlashDevelop user, so I've a little bias towards it. Lately, I've been trying to look at FlexBuilder with regards to its strengths. I've found that if I am doing a lot of MXML coding, FlexBuilder is a better tool. You have a class view of the MXML and it is good about hinting for MXML attributes. If you need to do absolute positioning, FlexBuilder also wins because of it's WYSIWYG editor.
But when it comes to ActionScript 3 coding, I'd much rather be in FlashDevelop. FlashDevelop's code hinting is much more powerful, for example it does NOT require you to type exactly the right characters. It's a breeze to jump around to declarations of code as well as nice features for creating getters/setters, promoting local variable to member variables, and creating event handlers. The look and feel of FlashDevelop is also nice, it launches and runs quickly. It has good defaults, a user-friendly UI, and good choices for fonts (I guess that could fall under "good defaults"). FlashDevelop is also free.