He missed the cascading kicks. Therefore, even waking up out of limbo wouldn't take him directly back to the real world.
But with everybody else already awake, those other dream levels may not exist anymore (since they weren't Cobb's or Saito's dreams). The real world may be the only place left to go.
We may not have ever actually seen everyone else wake up. We saw them get back to the first-level dream. The wake-up scene could have been part of Cobb's alterna-limbo.
However, you do make a good point about the lower dream levels dissolving when everyone leaves them, so it seems that even if Cobb is still dreaming, he's now only 2 levels down at most, which means the limbo state could only last for months (rather than years) before he woke up anyway.