PHP includes structure

For over a year now, I have been using PHP includes
and requires in my headers, footers, menus, etc. Each
page in a site was named with the extension .php and
then I would insert various common content into each
file I created. For structure changes, I still had to
go into each page and make the changes.

I recently made a jump in intuition and began building
a new site the other way around. Essentially it is
just one HTML coded page where all the links carry a
variable in the URL identifying the content - almost
like frames. As I kept going, I even added the secure
login areas into the single index page.  The only full
secondary pages I created were those using the SSL. 
The main page has a long list of IF structures that
plug in the content from files named
something.inc.php.  I find it so much easier to work
with, validate and update! All HTML changes are made
on the one index.php!  I have already re-structured
two other sites this way.  

My question is simply if this is so easy, am I missing
something?  I haven't seen this setup discussed
before.  Is this setup stable for even very large
sites or are there some issues with this structure for
search engines, etc? I'm aware of the caution to
ensure that the includes end with .php to ensure they
are parsed.

Thanks in advance, Fran


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