I have used the annex checkpoint and walked back; while the line is usually shorter, there are also fewer staff, so it can be hit-or-miss. What's really frustrating is that you can't get a sense for how long the line is at the main Term A checkpoint until you get upstairs, and by then it's just too late.

I, too, have found RDU to be fairly slow checking in; there's usually an idle station regardless of how long the line is. SEA comes close in terms of length of line for me, although it moved fairly crisply.