Here's my take. I keep seeing a lot of the same questions, so hopefully this explanation can answer a lot of them.
For the purposes of analysis, I'm going to assume that the plane level is actually reality, whether or not that's true. If everything's a dream, then there are really no rules, and anything is possible.
Secondly, I'm also going to assume that limbo is a state of consciousness, not a specific dream level. Limbo is simply the place you go when you lose track of the fact that you're dreaming. It could therefore be assumed that "normal" dreams are limbo states, albeit far less powerful ones than the ones depicted in shared dreams. It is relatively simple to escape from limbo: you just have to die. However, this is a much more terrifying prospect in limbo because, by its very nature, limbo means that you believe you are dying "for real." Think of the "waiting for a train" scene: neither Dom nor Mal was completely sure that their world wasn't reality, so it was very hard for them to lie down on those tracks.
Chronology:
Reality: Everyone is on the plane to LA, connected.
Level 1: City streets. Yusuf stays awake as everyone else descends into level 2. Everyone else is connected to each other. Saito is dying.
Level 2: Hotel. Arthur stays awake as everyone else descends into level 3. Everyone else is connected to each other.
Level 3: Mountain fortress. Eames and Saito stay awake. Fischer is shot and descends into level 4 (which is limbo for him, because he cannot tell that it's a dream). Dom and Ariadne connect to Fischer and descend into level 4.
Level 4: Dom's world. Dom uses his old dreamworld to house Fischer's subconscious.
Level 1: Meanwhile, Saito dies in level 1. He is not connected to Fischer/Dom/Ariadne in Level 4, so he enters his own, separate limbo state. It could be considered "level 4b."
Level 4: Ariadne tosses Fischer off the balcony. He dies, sending him back up to level 3, where...
Level 3: ...his subconscious arrives just in time to fill his newly resuscitated body.
Level 4: The weather goes nuts and Ariadne throws herself to the wind as...
Level 3: ...the building collapses, kicking her back.
Level 4: Dom vacillates about staying in the limbo state with Mal. Presumably, he does ultimately escape, probably by dying. He does not, however, ride the kick back to level 3 with Ariadne.
Level 3: Just as the building's exploding...
Level 2: The elevator explodes upward, kicking Fischer, Ariadne, and Eames back to level 2. Simultaneously...
Level 1: The van hits the water, kicking Eames, Fischer, Ariadne, and Arthur back to level 1. Eames becomes Browning once again so he can go see whether the inception took. Ariadne and Arthur are distressed because Dom does not wake up. Dom drowns in level 1, where he is still connected to Saito. Therefore, when he finally escapes from level 4, he enters Saito's limbo state with him.
Level 4b: Dom is unsure of whether he's in reality, but somehow he can instinctively find his way in the limbo state, possibly because he's been in a similar situation before. He must convince Saito (and himself) to commit suicide. Presumably he is successful, because...
Reality: The drug wears off. Everyone, including Saito and Dom, wakes up, alive and well.
I think that covers just about all of the major questions and "plot holes."
For the purposes of analysis, I'm going to assume that the plane level is actually reality, whether or not that's true. If everything's a dream, then there are really no rules, and anything is possible.
Secondly, I'm also going to assume that limbo is a state of consciousness, not a specific dream level. Limbo is simply the place you go when you lose track of the fact that you're dreaming. It could therefore be assumed that "normal" dreams are limbo states, albeit far less powerful ones than the ones depicted in shared dreams. It is relatively simple to escape from limbo: you just have to die. However, this is a much more terrifying prospect in limbo because, by its very nature, limbo means that you believe you are dying "for real." Think of the "waiting for a train" scene: neither Dom nor Mal was completely sure that their world wasn't reality, so it was very hard for them to lie down on those tracks.
Chronology:
Reality: Everyone is on the plane to LA, connected.
Level 1: City streets. Yusuf stays awake as everyone else descends into level 2. Everyone else is connected to each other. Saito is dying.
Level 2: Hotel. Arthur stays awake as everyone else descends into level 3. Everyone else is connected to each other.
Level 3: Mountain fortress. Eames and Saito stay awake. Fischer is shot and descends into level 4 (which is limbo for him, because he cannot tell that it's a dream). Dom and Ariadne connect to Fischer and descend into level 4.
Level 4: Dom's world. Dom uses his old dreamworld to house Fischer's subconscious.
Level 1: Meanwhile, Saito dies in level 1. He is not connected to Fischer/Dom/Ariadne in Level 4, so he enters his own, separate limbo state. It could be considered "level 4b."
Level 4: Ariadne tosses Fischer off the balcony. He dies, sending him back up to level 3, where...
Level 3: ...his subconscious arrives just in time to fill his newly resuscitated body.
Level 4: The weather goes nuts and Ariadne throws herself to the wind as...
Level 3: ...the building collapses, kicking her back.
Level 4: Dom vacillates about staying in the limbo state with Mal. Presumably, he does ultimately escape, probably by dying. He does not, however, ride the kick back to level 3 with Ariadne.
Level 3: Just as the building's exploding...
Level 2: The elevator explodes upward, kicking Fischer, Ariadne, and Eames back to level 2. Simultaneously...
Level 1: The van hits the water, kicking Eames, Fischer, Ariadne, and Arthur back to level 1. Eames becomes Browning once again so he can go see whether the inception took. Ariadne and Arthur are distressed because Dom does not wake up. Dom drowns in level 1, where he is still connected to Saito. Therefore, when he finally escapes from level 4, he enters Saito's limbo state with him.
Level 4b: Dom is unsure of whether he's in reality, but somehow he can instinctively find his way in the limbo state, possibly because he's been in a similar situation before. He must convince Saito (and himself) to commit suicide. Presumably he is successful, because...
Reality: The drug wears off. Everyone, including Saito and Dom, wakes up, alive and well.
I think that covers just about all of the major questions and "plot holes."