You can use FP, without using anything that depends on the FP extensions and by editing the CSS yourself, to build sites that don't look like FP and work fine.
I still use FP for low budget sites and find it more productive for simple sites (but more limiting) than the "pro" web wysiwyg editors, once you understand the program.
FP includes are OK to use and I've never had a problem with the regular text mouseovers or image maps(but have with the "hover button" rollovers).
So, If you MUST use FP, just make your own nav in a table, instead of using their "shared borders". You can even use their block diagram thingy. If you turn off "add to navigation" on each of the pages in the block diagram, FP won't try to create a nav system.
And (as stated above), you can create, add, delete or modify the graphics and colors and fonts of an FP "theme" as much as you like - and even save it as a new official FP theme. Or use no theme and just do your own "look".
I like to have a text only list of links at the page bottom, you know - the traditional "¦ Home ¦ About Us ¦..." sort of thing (in an include) for the robots and the occasional human that needs them.
My favorite layout is the one FP uses (they did their usability homework):
-Nav column on left for local folders and subfolders
-Logo and page Title along the top
-Nav along the top for links that should always be accessible from any page
But, I like to do a breadcrumb trail across the top as well.
I also like just having every available link to every page in a left column and no nav on top, if the site is small enough.