First and foremost, as it has been mentioned before in years past, is mod API integration with vanilla. It's long been agreed upon, and let's be honest here, that if Mojang made or acquired a mod API, Forge would be able to do it many times better.
Then you have the chances of dealing with people installing potentially malicious content on servers, or trackers.
That said I'd have no problem with the FML developers to take this up. I'd be completely onboard with the idea otherwise.