I agree that pantheon bloat could be a problem, and IS a problem (I still don't know all the LEW deities... or Eberron deities, for that matter).
I really think a list of seven to nine deities, AND NO MORE, would be great. We can add minor angels, saints, and demon gods later on, that are mechanically similar to deities. But keeping the initial god list low is an excellent idea.
However, connecting that to the PHB might be a poor idea. I really don't want to see followers of Pelor, Kord, and Bahamaut in L4W, for the simple reason that those gods are D&D expectations, and not OGL expectations. D&D is a seperate beast than a pure SRD game, which is something I think a lot of people notice after they've played their first PbP.
I think we should try to seperate ourselves, if not mechanically than stylistically, from the core books. Adopt a greek feel and model (something I'd totally be for). No Mind Flayers? No Problem. And all that.
While learning the pantheon could be tricky for new players, I think most people get the hang of it really quickly. Though, a lot could be said for simply adopting the Greek or Roman pantheon, names and all, and running with that.