It's the most story-driven of these three mini-series. It's telling a major storyline about Doctor Doom that wasn't hinted at in the other two and for a while was threatening to take the series in an incompatible direction. That's pretty cool, although everything ties together eventually. (After extremely dark plot developments.)
1.
Marvel Universe vs. the Punisher was a character study of the Punisher himself, with a plot built around his ongoing war against the infected and his questionable level of interest in saving the human race.
2.
Marvel Universe vs. Wolverine didn't give Wolverine that much agency. He's written well and it's definitely worth reading, but it's telling the story of how the original outbreak took hold. That's not a storyline that gives fighters much control over anything. The world goes to hell and your friends might become mass-murdering cannibals at any moment. Combat abilities don't mean much any more, except in the short-term sense of trying to keep more important people alive. The people who'll make a difference are the brainboxes investigating a cure and it might have been more honest to call this Marvel Universe vs. Reed Richards.
3. This mini-series, on the other hand, asks the Avengers one hell of a question and then follows through on it. Imagine that civilisation is disintegrating in something akin to a zombie apocalypse. Imagine a legendary genius appears, promising to be your saviour. Unfortunately, he's Doctor Doom. Do you bend the knee and obey? Should you trust him?
(Hmmm. What if Doctor Doom's problems mostly come from his grandiose choice of name? If he became a GP, patients would keep transferring to other practices. They'd have a lot more faith in him if he called himself Doctor Nice or Doctor Fluffy Hearts And Unicorns.)
The protagonist is Hawkeye, although this is an ensemble piece and "vs. Avengers" is an appropriate title. I liked this Hawkeye. He's got no superpowers. He's just a tough guy who knows archery. That's a good fit for this series. Mind you, he's a blend of different versions of the character. He's mostly his traditional Marvel self (i.e. before they got into 2010s dreaded "movie synergy"), having his original outfit and gimmicks and being an Avenger. However, he does black ops for S.H.I.E.L.D. and reports to Nick Fury, which is from the Ultimate Comics that influenced the MCU movies. When this comic book was published, those were current, fresh and probably higher profile than the original Marvel-616 version.
The ending's comparable in Oh My God bleakness with the Punisher's, albeit in a different way. I see alternative interpretations. Is that a Night of the Living Dead ending, or was a certain person genuinely infected?
It's pretty good. It's asking "can you trust a supervillain?" That's primarily Doctor Doom, but even before that enemies had been co-operating against the infected. Supervillains join forces with Hawkeye and Howard the Duck (yes, that's right) in Central Park. I couldn't find a graphic novel for this one and bought the individual issues, but Marvel should release a 300-page collected volume with all three mini-series together. They're one combined story, after all. It's just three perspectives on it, each different enough that it's fine to read the three in any order. This is the least time-jumpy of them, actually. (I'm normally pernickety about reading order, but in this case story order is up for grabs since Wolverine's comes both first and last, thanks to an epilogue.)
If you're looking for something horrible, shocking and flesh-eating, give this little "What If" not-a-zombie universe a go. It's a lot nastier than I'd expected.