By putting content inside a Flash applet you isolate it from the web. It cannot be crawled. It cannot be deep linked to. It cannot be styled as the user prefers, rendering it inaccessible to disabled users.
Flash is not a web technology. It is anti-web. It may as well be a zipped .exe, served up over Gopher. The simple act of placing content within an SWF file is tantamount to secession in itself.