The fees are coming, there is no doubt in my mind.
These large companies have bought up all the game studios and only care about making money. All it is takes is someone like Activision, EA, or Microsoft to make a profit off of a $2 a month fee and the rest of the big companies will follow!
$2s might not sound like a lot, but there are a million+ gamers online at any given minute in the world. Even if 3/4 of us walk away from our favorite game (doesn't have to be COD), they will still make a killing off the people who don't leave.
Hopefully we will see some of the good gaming studios go indie (or rogue) and we will still get some really good games. For instance, like you said Bungie, who left Microsoft.
But then, look at InfinityWard and Activision, we will never really know what happened behind those closed doors. These big companines have no problem buying a well-known studio for a game franchise and firing all the top management that push out a good product. They will take a good game, make a few changes, repackage it, and push it out the door for $60 a pop. Look at the last three COD games!
This may still be a few years away, but it is coming...
:(