Where is the thing I can do as a rogue, or a wizard, or a fighter, that no one else does? It's not my combat role (others do that, though in different fiddly ways), it's not my out-of-combat role (others are basically my equal in this regard). What do I contribute to a party that is binary? That is "Oh, you don't have a Rogue, so you're going to suck at X."
I think this is a harder balancing act than even "power acquisition" rules, because part of 4e's philosophy is that everyone can contribute in some meaningful way all the time. Which isn't a bad philosophy, because it's boring sitting out a challenge you can't contribute to.
I dunno...there are some things that would alleviate the issue before we got to that point, I think. And maybe some sort of expanded roles system or whatnot is useful (In combat, a rogue is a striker! In exploration, the rogue is a trailblazer! In social situations, a rogue is a wit! The rogue is the only class with this unique combination; other classes have other combinations!) in just creating levels of difference.
The more things I can point to on my character sheet and say "I am the only character who can do this," the better the class variety gets, I think.
Which brings us to the OP. I don't think this is an insurmountable problem for 4e. Heck, talking like this, it seems that 4e could even probably accept some add-on systems to mostly solve the problem. And those that don't have a problem don't need to use any of the sub-systems.
Hmm...brain churning...
The problem (referring to the above something that only x can do) with this is that you can easily end up with circumstances that negatively impact the game, all for the sake of niche protection.
A prime example of this was 3.x rogue Trapfinding (which, IIRC, stated that only classes with trapfinding could find traps with a DC 20 or higher- most traps). Your character could be a master trap maker with a +50 search check, but unless you took a level of rogue (or one of the few other classes with Trapfinding) you could locate only the crudest of traps. It neither made sense nor benefited the game (IMO).
It was problematic because if you didn't have a trapfinder in the party, traps became that much more deadly (most DMs I knew simply would avoid using them without a trapfinder, because we weren't the biggest "Gotcha!" fans).
I think that a better approach would be to accentuate something that a particular class excels at. For example, rather than declaring that only rogues can find traps I think it would be better for the game as a whole to simply give them a bonus to finding traps. Of course, the pitfall of this is that it can easily lead back into the situation where either the rogue is the only one who can find the trap (because the DC is adjusted for a rogue with trapfinding) or the rogue automatically succeeds at trapfinding even when blindfolded (the DCs are calibrated so that anyone has a chance for success).
One solution might be to offer the rogue a small bonus (such as a +2 which doesn't much unbalance the DCs), or a feature that guarantees he's one of the characters with the highest trapfinding ability (such as allowing him to use his highest ability score in place of Wisdom when searching for traps) to reflect his expertise, but I imagine most would consider this insufficient differentiation.
Another possible solution that I've toyed with in my head would be to offer non-combat add on features (I think of them as Kits, akin to 2nd ed) that allow PCs to do something that they previously couldn't do. One example would be a Noble who is automatically able to call in favors (on a limited basis of course) based on his family's prestige (the other PCs could still, of course, earn political favors to call in, the noble simply gets bonus favors for "free"). The biggest challenge that I can see for this is simply thinking of enough interesting new "abilities" that don't step on the PCs' capacity to adventure normally (in other words, avoiding things like the aforementioned Trapfinding).
As a parting note, I would like to point out that 4e does already possess such features to a limited degree. For example, the Rogue Level 6 Utility Power, Chameleon, grants him a chance to remain hidden when another creature gains line of sight to him. That is something that no one else can do.