I do not know how this would fit in the timeline :( but looking at pager.inc overall I thought it may be worth to build a component for the helper functions and to move the pager theme preprocessing to theme.inc.
I will post a first stab - a patch that eventually removes pager.inc and 4 global variables; also, makes a bit more readable the routine that prepares the 'page' querystring fragment.
I have incorporated parts of #1588138: theme_pager() overrides parameters passed programmatically in this patch.
Of course more polishing would be needed, but before all I'd like to get feedback: is this a path that make sense to follow?