Yep. There are some nice features like exporting as an XFL, but for the most part, SWF export is limited.
https://help.adobe.com/en_US/AfterEffects/9.0/WS3878526689cb91655866c1103a4f2dff7-79caa.html
File size will always be smaller out of Flash, but I suppose it comes down to what my client wants: Small, fast loading web vector SWF’s or slightly longer loading FLV’s with video footage and bitmap graphics.
— Tony
Tony W