You can use the Plugin feature of Framework builder to leave behind DWTs and work solely with conditional includes in the current version.
However DWTs are actually given new powers and the limitations are stripped away for the most part with the Theme feature of framework builder... so you may find them useful again. The only real ties to the template are that it looks at it to find the design. The template editable regions are just used as xml markup to determine which areas to replace... the drawbacks to using a dwt are vertually eliminated.
Technically it doesn't even really have to be a template... it just needs to identify editable regions where content will be gotten from the page... however dreamweaver assumes you want a template at that point so it saves it as one and changes the extension to .dwt... but since no pages are actually derived from the template itself it functions like a page and not a template.