The only idea for multiplayer I could think of that would be interesting, beyond a co-op campaign, would be a Horde mode style or maybe a Left 4 Dead style co op mode where you either have to fight off enemies, or make your way from one point to another while contending with enemies, BUT, keep the same idea of low ammo counts, stealth, and melee/improvised weapon combat.
If done right, it could be awesome, and I just pulled that idea out of my ass. Naughty Dog has had years and plenty of cash to come up with something, so I have high hopes for what it could be. It's not like it was a last-minute addition- they probably started with multiplayer as a core feature from the outset.
Also, one of the ND guys was on a recent episode of Weekend Confirmed (last week's, I think) and was talking it up. Sure, he could have been fibbing, but I still think it'll be original and good.