I have thought alot about this too and it is a very perplexing question. Being that I am primarily an FPS player I like any MMO that folds in FPS mechanics.
In FPS it is completely possible to sneak, just stay out of people line of sight and be quite. If someone isn't looking for you it makes it even easier. I don't think this alone will work in an MMO setting, but maybe a mixing of the two will work.
You're "sneak" relates to how stealthy you are, Your understanding of shadow and sound and gives you more ability to be unseen. So, why not actually make this function that way. The higher a persons Sneak skill the less visible they are, Until they master Sneaking (what ever number that may be) and are practically invisible. This could be augment of course by stealth boys or gear meant for stealth.
To counter this one's perception would allow you to see or hear a person trying to sneak more. Not everyone's eye sight and hearing is the same so people would have a harder or easier time spotting an intruder if they had good perception.
So with this kind of system you have a scalable opposition system that makes level and skill points count, but at the same time keeps the game play fresh and makes individual player skill count too.
Address the MMO leveling side and the game play skill side.
I would be very happy to see this in an MMO, especially a game that uses SPECIAL. Another drunk conquistador conquering the governor's ball...