But then Wreckers came along. And then Chaos Theory, which, when you think about it, deserves its own special award for wiping out every origin story from the ****-stain of Megatron: Origin to the relatively good fun of War Within.
And then MTMTE blew the entire thing out of the water.
So, here's my revised list. What constitutes a comic story arc? For the purposes of list-making, I decided to qualify an "arc" as "a conventional trade" meaning anywhere from 3-12 issues. I know that digital comics have changed things, but I needed some break.
So I can't, by my own rules, count all of MTMTE, or T:2006 through Time Wars, or Matrix Quest through Edge of Extinction, as one arc. I have to count individual component stories (Liars A to D, Space Pirates, Matrix Quest).
5- Shadowplay
I struggled over the best way to parse out MTMTE, and I kept coming back to Shadowplay because it is such a neat, tight arc that speaks so much to the world outside the Lost Light. Not only do the characters advance in the present, simply by talking, we see where they came from, we see more of Roberts' pre-war Orion Pax (the very best Optimus Prime ever written, anywhere in TF fiction) and we get a ton of world-building. Empurata, shadowplay, relinquishment clinics, the Institute, the origin of Shockwave and the subtler origin of the Autobots themselves all within a damn good heist story. Also, some of Milne's best art in the Cybertronian sequences. One is reminded why Pat Lee paid the guy to draw his backgrounds.
Honorable mention: MTMTE issues #1-6, for introducing the Lost Light crew and for a Ratchet story that actually surpasses "Warrior School."
4- The Unicron Saga (Eye of the Storm through On The Edge of Extinction)
I don't have to say what's great about this--I just need to justify why it's at #4 and not #1. But I will say that this story worked, for me, because Simon took away the McGuffin. Suddenly Autobots and Decepticons had to make peace, and Scorponok had to think beyond his typical schemes, and we didn't have the potentially neat clean ending of the Animated Movie.

3- Chaos Theory
The speech-as-climax thing is hard to pull off. I thought that, after Buffy season 7, I could never take another speech. I was wrong. You see, when Orion Pax has just shown how badass he is (how badass is he?) by riding his dead comrade over the Senate stooges, I will listen to anything he says. But of course, this story goes farther by showing just how alike Prime and Megatron are, and how much admiration Prime has for Megatron. Megs' own convictions make a Prime out of Pax, and I love that--it shows how the rest of their relationship has been based on Optimus' respect for his foe. James made the entire Decepticon/Autobot war interesting by rooting it in a corrupt society.
2- Last Stand of the Wreckers
Maybe it was the times, I thought. Maybe it was the fact that this comic came out at the nadir of IDW's run, accompanied at the story by Costa and the Bayformers and Plight of the Bumblebee: Expanded Edition. So I went back and read it. And read it again. And bought the hardcover and read that. This story does a lot of what Shadowplay was to do--expand the TFs' world--but it also makes us care about red shirt TFs, in relatively little space. Ironfist, Rotorstorm and Pyro will never seem the same. Aequitas goes down as one of my favorite comic reveals ever, given the way that it played into the Wreckers' own shades of gray. [edit] This goes at #2 because, unlike Roberts' other stories, the stakes are bigger and the deaths hit harder.
1- Generation 2
A controversial decision, yes? But for me, TF comics are big-idea space opera. It doesn't get much more big idea than this. Simon irreparably ****** the Autobot/Decepticon dynamic. I love how, even at the end, with the Swarm closing in and the Cybertronian Empire destroying whole cities, Starscream's ambition nearly destroys Optimus and Megatron's alliance. The TFs really are their own worst enemies whenever a story demands an alliance. All good TF stories end with some upset to the status quo, and nothing quite tops Geoff's final rendition of the Liege Maximo, sitting on his throne. It was as if Simon dared me "go on, imagine what else could happen..."