So you're not supposed to worry too much about the logic of the dream levels, since all dreams are basically metaphors for life: mazes where people "get lost" and from which they need to "die to wake up". The only thing that makes limbo special is that it is particularly symbolic. Nolan is presenting a metaphor of life itself as a Penrose staircase, and portraying faith as the way out. When Ariadne shatters the mirrors that trap Cobb in a recursive chain, the image is symbolic: she is a gift from Cobb's father ("ask and ye shall receive") and her role in the film is to guide him out of the maze that is the mortal world. This is presumably why she is the character who accompanies him to immigration.
For more evidence that this is intentional, look at the overwhelming creation imagery and the narrative emphasis on father-son alienation and reconciliation (with Fischer as with Cobb). Look at the curious way Michael Caine seems to be playing God when he shows up in Paris. And then look closely at the ending, which shows us neither a dream nor reality. What Nolan presents is symbolic: we see Cobb's judgment and forgiveness of sins at immigration, and then his reunion with his family in the heavenly garden. The film closes with Cobb ignoring his totem (as a crutch of faithlessness it is no longer needed) and then his son James (who represents faith and like his sister shares an apostolic name) telling him that they are building a castle on a cliff.
A what? That last bit circles back to the opening shot of the children on the beach. It is a bookend reference to Matthew 7.24 and the parable of the wise and foolish builders. The contrast (beach -> cliff) reinforces Cobb's character journey while telling us that the ending is NOT a dream (something reinforced by the lack of the water imagery associated with the other dream levels). It also reinforces the parallels Inception creates between the buildings of limbo and the sandcastles on the beach, and explains why all are ultimately washed away by water just as death washes away life in the Christian parable.
Brilliant movie.
So where is the problem? Nolan himself has said in media interviews that the significance of the top is that Cobb walks away. He's also remarked on the centrality of creation imagery in the film and explicitly stated that "there's a relationship between the sand castle the kids are building on the beach in the beginning of the film and the buildings literally being eaten away by the subconscious and falling into the sea." Funny how he even specified the beginning of the film in that quote. No-one is post-rationalizing those words into his mouth.
Frankly, there's tremendous power to any interpretation that leads one independently to the same conclusions the director later makes, all the while explaining away what are inconsistencies under other readings (why Mal is bad, why the continual biblical references, why there is so much damn water in the dreams, etc. etc. etc.). The fact that Nolan is using fairly conventional symbolism (water = death/subconscious) is just icing on the cake.
We know Cobb doesn't need his totem by the end, because his rejection of Mal at the climax is an expression of faith. To understand the implicit alternative, look to the parallel heist sequence which opens the film. There we had a very different Cobb place his faith in the "reality" of Mal when he lowered himself out the window above a fatal fall. Nolan emphasizes that this is the wrong decision by showing us Cobb's immediate (biblical) fall, blasphemy and then betrayal and loss. Death destroys the world by water as foreshadowed in the parable that opens the film.
At the end of the film the logic of this sequence reverses. Cobb resists Mal's temptation to stay with her in limbo. He rejects her for the first time ever, telling Mal she is not "real" where even moments before he was expressing lingering doubts to Ariadne ("how can you know"). And whereas his lack of faith had previously led to his defeat, here his expression of it leads directly to Fischer's symbolic reconciliation with his father. And while the film presents another death sequence as required by Matthew 7.24, this is but prelude to a heaven sequence that breaks the endlessly circular logic of the dream world / penrose staircase. The rules are violated because they no longer apply: Cobb is free of the maze.
Though I still think that the ending scene is badly handled. If the point is that Cobb doesn't care any more about the outcome of the spinning top, then Nolan should have just slided from the image of the top to Cobb and his children.
By zooming in on the top and cutting the shot right before it should falls, it just adds this unneeded baggage of questioning whether all that happened is real or not. Like some sort of magic trick. "Do you doubt what you've just seen?" And I just didn't find that that was the point of the movie.
So Inception might not be for everyone since it's heavy on narrative and light on character development (we don't see why Cobb changes, he just does), but there's all of this wonderfully meta sleight-of-hand just below the surface as Nolan tells us how he is making the film. Even beyond the symbolism, the very rules he outlines for how to create dreams apply equally well to the film itself (make the plot a paradoxical maze, get the audience lost in it while you plant ideas in their heads, and make the message stick by forming it around a core message of positive emotional catharsis). And yet we are still surprised, or I was at least!
Anyway, hopefully if you see it again you'll like it better next time. I personally think it's hands-down one of the best films in the last decade, and it's a real pity it got shunted off at the Oscars when it should have swept the field.
I'm surprised that Memento didn't make your Christopher Nolan short-list. Perhaps you didn't care for it, you haven't seen it, or you simply forgot to add it.
If you haven't seen it, I highly recommend it.
I think though that we can go a step forward.
I agree that we all should look at it much more in a symbolic and metaphorical way than a logical way (there are several points in which the internal logic is severely weak).
And exactly because of all the reasons you mentioned above, I've always considered the whole movie being representing something related to Cobbs.
Cobbs is the one receiving the Inception.
No matter if by God or Ariadne, or God through Ariadne or viceversa. Or if this happens in the real life, afterlife, parallel life, dream levels or what. The whole movie is about Cobbs and his subconscious. It's also interesting that Nolan used the name Cobbs for one of the characters of his first movie, Following, in which Cobbs was some sort of serial burglar. Just to keep the metaphor going.
With the first name Dominick ("belonging to God") no less! Tons of this stuff in the script -- amazing that Nolan lost best original screenplay to The King's Speech. The mind boggles.
3) The sedation is the difference. Cobb and Mal weren't sedated when they were in limbo, so killing themselves worked to wake them up. In this case, Fischer's under heavy sedation and dying wouldn't wake him up, even from limbo. Hence, the defibrillator was used to 'kick' him up from limbo to level 3.
He was dreaming ever since Yusuf demoed the sedatives the first time, showing lots of people who dreamed all day (the "no, they come here to wake up" scene).
Fisher tries to check his totem at that time but can't do it because he's trembling so bad.
Thus, if he were under sedation, dying would not wake him, though my argument doesn't explain how he moved up multiple dream levels to the plane...
The dilution of the gravity effect seems consistent with exponential expansion of time.
1. The bulk of the story is framed as Cobb & Saito's recollection in limbo. My theory is that the recollection (rather than the gun) is what wakes them up.
2. There is no explanation for why the first kick in dream level 1 (the one they miss) doesn't wake up Arthur, who is awake in dream level 2.
1) It is never said that 3 levels is the maximum depth of a dream until Limbo occurs. My interpretation has always been that Cobb and Ariadne hooked up a shared-dream machine to Fisher's dead body, which brought them into Limbo.
2) Why are there 2 Limbos? There's the one Cobb and Ariadne follow Fisher and Mal into (which has the architecture of the Limbo that Cobb and Mal shared all those years ago). There's then the Limbo that Cobb and Saito share, where it looks like Saito architected the environment (Asian influences). And if they were the same Limbo, why was Cobb washed up on a shore with no memory of how he got there in Saito's Limbo?
3) In the Limbo that Cobb and Mal shared, all they needed to do was kill themselves to wake up. Why then was the defibrillator needed to wake Fisher up from death in Limbo to Dream 3?