I've tried to work this out before, but I think the key to booking like they do and still getting people over is to adopt something similar to the old All Japan system, where you have loosely organized groups of guys with a hard kept hierarchy. 2/3 top level faces, 2/3 top level heels. Underneath each is a US title tier guy and/or an IC title tier guy, a tag team, and maybe a low card/job guy. You don't present them as a group, the way WWE usually tends to, but for tv you run lots of tags and six mans, etc, and this is where your pairings come from. You enforce the strict hierarchy in that you keep apart your 1 vs 1 and maybe even 1 vs 2 matches on tv. Same with 2 vs 2, 3 vs 3, etc. You build those rivalries through tag matches, etc, and save the equal matches for something with a payoff. When you establish this order, you can effectively build guys by booking the upsets. The upsets need to have meaningful changes to the depth chart, though. Guys moved up, guys moved down.
I have no idea if this makes sense. I'm at work, and have written this in several intervals. I'm trying to put together a depth chart, but the current roster makes it hard.