Well, I've read many a reviews and theories already so here's mine:
I think this season was leading up to the great reveal of what the "Revolution" is and why every "bady" has made mention of it. Moreover, why once it is started it cannot be stopped (ala Zaheer). There's lots of reasons for this and I'm going to break it down by working backwards. Let's look at Korra's hallucination induced visions.
We see Amon, Unaloq, and Vaatu.
On the surface, this doesn't seem odd. All these folks tried to kill her, and came very close. However, we should know by now that nothing is as it seems, as in the Avatar world as it is in reality.
Vaatu - of course he is a source of fear and nightmare. He was, by all right, her absolute opposite. Raava and Vaatu, yin and yang, equal opposites. The fact that the Avatar is both Raava and a highly skilled and trained human gave the upper-hand in Vaatu's apparent defeat.
Unaloq - Sure, he's a reasonable source of fear. He unlocked Vaatu and bonded with him, right? And hey! He's a part of the Red Lotus, which is everything Iroh and the other White Lotus once tried to prevent.
Amon - ....wait. Amon? Why Amon?? He has nothing to do with Vaatu or Unaloq. He wanted an end to benders, he wanted there to be an absolute separation between the spirit world and their world, thus creating equality and peace among all people. That's...the opposite...isn't it? He took away Korra's bending, and left her really psychologically damaged for a while because of it but it's not like he was coming anywhere near the goals of those to come.
Now, way back when in season 1 Tarrlock explained Amon's life story with a big obvious gaping hole. Amon went M.I.A. until he resurfaced as the Equalist leader. As the leader, he proclaimed that a spirit gave him the power to take away bending. Apart from the Avatar, the only other source of giving and taking bending comes from the Turtle Lions, and Vaatu and Raava. And how do we know this - when Korra got a look back to the time of Wan. Again, Amon said it was a spirit. Sorry, Turtle Lions...not this time. So, given this, how can we be so sure the hallucination induced visions were wholly the poison as she bounced back and forth from the avatar state?
Let's map this one out a little, flushing it out with what might be some missing pieces:
Raava and Vaatu entangled
Raava and Wan bond. Literally
Enter Avatar Wan
Vaatu is locked away for a REALLY long time
Vaatu gets to sit and plan until the next harmonious convergence...which is a REALLY long time
Avatars come and go through generations
Bending develops a dark side (blood bending, etc)
Noatok and Tarrlock learn to bloodbend
Noatok runs away at an early age and meets up with the Red Lotus
(probably around the time Zaheer and friends were there, P'Li having been recruited as a child as she described)
While with the Red Lotus he (and possibly Zaheer and friends) go with Unaloq and meet Vaatu
Noatok sees the Avatar as having too much power
Vaatu teaches Noatok how to take away bending
Unaloq and Zaheer et al have a falling out and go separate ways
Noatok, as he had with his father, sees benders as corrupt
He flees and adopts a mask and false identity (Amon)
Meanwhile, at some point, Zaheer et al are imprisoned
Amon goes to the other extreme of no benders, having seen what they are capable of through the Red Lotus.
Tarrlock gives the background on Amon's true origin
Amon is revealed as Noatok
The strife between brothers leads to their demise.
Member of the Red Lotus, he's busy ruling a nation and plotting worldly conquest
Vaatu deceives Unaloq, knowing an opportunity to escape is coming
Harmonic Convergence is nearing and Vaatu lures Unaloq deeper with false promises of power
Unaloq manipulates the Avatar to free Vaatu
Vaatu is free and begins to reign chaos over both realms
A big battle ensues of epic spiritual magnitudes
Vaatu is apparently vanquished
Along comes the spirits, and oh what a mess that is
Air Nomads have started springing up everywhere
Cool, there are four nations again! Balance? No. Chaotic? A bit.
Enter Zaheer and friends.
They try to kill Avatar Korra through poison (kill her in the Avatar state so she won't be reborn)
P'Li, Ming Hau, and Ghazan all die -and it's not at all unclear, yikes!
Zaheer is trapped in a stone brace (much like Ozai long ago)
Zaheer declares the Revolution can't be stopped once it's begun...just before the comic relief shows up (Bolin).
So, here's what I think: There is something connecting all the villains thus seen. Among the things tying them, one would be the Red Lotus and the other would be Vaatu. They all spoke of a Revolution. But what revolution? At this point, if Korra isn't wondering that too...then this is one hell of a big hole in the plot line. I think Book 4 is finally going to reveal what the end game for the Revolution is and what exactly the Revolution itself is -- and I suspect it's a world without the Avatar. From Amon to Zaheer (from A-Z, lol) every "bady" has wanted to get rid of the Avatar permanently for once reason or another...to stop benders from ruling, to renew the natural order of spirits and humans, to create chaos and bring an end to all authorities. Whatever the reason, it sure does seem like the Revolution is the building of a world without the Avatar.