Can I change pager.inc theme? can I theme output of includes/pager.inc using drupal template system?

I want invert page links, I don't want any edit on pager.inc or CSS.

maybe invert items passed to theme_pager function
Not sure what you are asking here, you can override theme_pager() like any other theme function in Drupal. It is however quite a bit of code.

It's also relying on global functions, so you probably can't simply call the original fuction with reverted arguments.