If we go with the 'primary' team and 'secondary' team approach then one suggestion is if I trade a player on my primary team he stays traded as long as he is on my team that season. For example TEX is my primary I can trade Danny Darwin and he stays traded until be moves to MIL. This is unfair to the person picking up the Darwin because they will lose him, but it still may work in pratice. Or do traded players stay traded no matter what, unless they are dropped at which time the revert to their real life team. This could mess up secondary owners, but then that is the risk of secondary picking. As in I can pick the Red Sox, but Boggs was traded so I don't get him. :(
With the secondary teams being swapped around each year there will be player movement. A good as this idea is, it is still not up to par with the decade (genius idea) concept IMO.