Hi Jani,
I'm happy that the template pleased you!

For sure there is place for improvements and that is why I have launched
TMM (Template Manager Module) to enhance template as easily as possible
with "smallest" impact possible on already installed/customized templates.
I see that you have a few refinment to suggest for 2013... that is pretty good!!
I suggest you to use menu "Wish List" to do more "formal" demands as it will be
easier to remember... I'm on "an other planet" these times (Linux project).
So my memory could forgot!!
For your counter, most of the time the counter (as flag counter) user javascript
to count your visitors. Then, the better place to put a .js call is at the real bottom
of the page.... juste before the closing </body> (fewer impact on loading time).
Depends on what you really want, "cute flag" display or real stats, you could
consider Piwik for page by page detailed stats.
Regards,
Jacques