The 1.16rc10a public beta is already out since Friday:
AACW {public beta} patch 1.16 Release Candidate 10a - January 13, 2012
There are no changes to current campaigns or scenarios being worked on other than to fix events and discrepancies.
[Insert the mandatory notice of the ability to create your own mods here]
In general I do not know of any special goals or awards to gaining military control over any regions other than strategic and objective cities and those appointed through events; Wheeling and Pittsburgh are both stratigic. If you take a strategic or objective city you will get a message in the log stating that your citizens are very pleased with this and you will get some MN awarded--although this is not always stated in the log--and 1 VP per turn that you hold them; more if there is an event that states this.
I've end-run Jackson into Harrisburg PA, taking and holding it for several turns before my supply started to wain and I don't think I got any NM for this at all. It just disrupted the Union's operations forcing them to gather a force together to try to throw me out again, which never happened because I skedaddled before they arrived. I'm not sure of what in-game significance Harrisburg has, but while displaying 'Strategic Towns'--press '3' while displaying the map--it's region is colored, but it's neither strategic nor an objective. It is the capital of PA in Real-Life™.
I think that strategically in the game, the importance of West Virginia for the South is to be able to threaten Wheeling and Pittsburgh. As the Union I almost always put a depot in Pendleton WV with a division and another division in Grafton to counter this. In Real-Life™ I don't know that WV played all that big of a role in the war . Giving WV official statehood in '63 I think had more political value than anything else, sort of like the Union patting itself on the shoulder for finding a friend and showing that the Union was still working; but I'm no historian.