While I kind of see the Jeff/Annie chemistry on a superficial level, I really love the way the jaded cynicism of Jeff & Britta just bounces off each other. This was especially clear during their drunken wedding toasts in "Urban Matrimony & the Sandwich Arts."
As for Jeff's less prominent role on the show, I suspect one of the big factors in that was the way that Abed's popularity totally took off. I doubt anyone saw that coming.