MLB made something like six billion dollars last year, and I don't know what sort of revenue sharing they have (if any), but there should be some sort of cap/floor. The problem is that players would definitely be against a cap, while enough owners would definitely be against a floor that neither has a good chance of happening anytime soon. It's hard to argue for a floor when teams like the Marlins can compete (and even win) every few years with such a small payroll. People can say that a floor would help the competitive balance, but there's enough of a legitimate argument against it that there's virtually no chance of either happening soon.
On the Manny investigations thing, I don't see how the commissioner's office could do anything other than suspend Boras or fine Manny. They can't nix the trade for the obvious reasons, they can't suspend Manny because all that does is hurt the Dodgers, and I doubt they would, say, award compensatory draft picks to the Sox. If they do find anything, I doubt they'd do anything more than suspend Boras. The players' union would probably fight against a Boras suspension because of what he does for the players. It would be a messy situation for all parties, so I don't think anything major will come from it.