After playing and GMing with several different PbP initiative systems, here's the one I've settled on for games I run:
I make all of the initiative rolls (saves a day/week/whatever of waiting for everyone in a party of six to roll/post). I average the rolls for each side. If anyone on the 'losing' side got a roll higher than everyone on the winning side, they go first in a sort of pre-initiative round. Regular initiative then starts, everyone on the winning side going and then everyone on the losing side. Actions are resolved in the order they're posted, eliminating almost all ret-conning.
This system rewards folks who take those feats and traits that improve initiative or have classes that do so both by raising the average of their team (thus helping the entire team as well) as well as by making it more likely that they'll get a roll better than everyone on the other team.