The ONLY thing I can possibly think of is that it would require the developers to code the 360, pc, and ps3 versions all in a way that prevents them from connecting to the same room. It wouldn't be that hard to implement a server browser in a game because it is obvious that the community will gladly pay the server costs. If you don't want them to just farm one map then don't allow specific game options. In the grand scheme of things that customization doesn't matter nearly as much as the ability to just play the game on a good connection. It would sell a ton more copies because it wouldn't be nearly as frustrating as it is now.
There would be an obvious issue allowing all 3 platforms to play together... That much is clear. The PC players would stomp on console gamers due to the superior precision of the controls and all three platforms could play together which would lower sales by making it possible to just play on your platform of choice which, in many cases, would just be a PC for the people who could do it because of the fact that the mouse will ALWAYS be a better aiming device. This would require servers to only host on a platform of their choice since it would be impossible for all 3 to work together. This would clearly cost a couple thousand in development costs which is just too much when you are looking at a multi-million dollar budget... I mean who can afford that when you are only given 10s of millions of dollars to rehash a game? That is just silly talk.
Console limitations make no sense to me because they could easily be so much more than they are. Yes, it is essentially a $500 gaming PC so you can't expect much but if you were to use dedicated servers to remove that extra burden, allow them to connect to the best possible one, and force those servers to follow strict guidelines you could have so much better gameplay.
Of course I am probably just insane because I also sit and wonder why, instead of paying for a new CoD title every year, they don't just develop one that allows for expansion and release mission packs, map packs, updates, and then charge like $2 a piece for new guns, perks, killstreaks, and clothing options... You could easily make more money that way than to blow millions on another rehashed title every year to hope to make that back and have enough profit to do it again next year.