If you're talking about using these extensions in public facing URLs, then I would say don't use either:
File name extension. This is a very
common one. "cgi", even ".html" is
something which will change. You may
not be using HTML for that page in 20
years time, but you might want today's
links to it to still be valid. The
canonical way of making links to the
W3C site doesn't use the extension.
(Taken from W3C URL style guide)
You can achieve this with mod_rewrite, for example.
However, if you're talking about how to name your files in the filesystem, it's largely a matter of taste. I think both the extensions you suggested (phtml and php) make sense, the main thing is being consistent.
Edit: Also, since you said this is for a framework, you should consider choosing a non-standard extension may require extra webserver configuration. For example, to support both .phtml and .php in Apache:
AddType application/x-httpd-php .phtml .php