rewatching S5 and thinking, actually, there's such an easy way to make Dean say yes and I'm genuinely surprised Michael has never thought about that. Maybe it's below Michael, because Lucifer has used the same trick four times and Dean himself used it once (four years later).
Apparently, vessels consenting to be possessed don't have to be true informed consent; the ones tricked by believing they're consenting to something else would also count. Lucifer pretends to be Nick's wife and Vince Vincente's girlfriend to make them say yes; Dean allows Gadreel to pretend to be Dean to make Sam say yes. And so there is such an easy and obvious solution to make Dean say yes in S5: if Michael pretends to be Cas.
If there's any angel in the world that Dean would say yes to, that would be Cas. Remember 05x13 when Cas passed out flying them back in time and spitting blood everywhere? And Cas also said even that is actually better than he thought, and when he flew back to the original time, he said he's surprised he made it. Which means, for all he knows, Cas doesn't think he'd survive that time travel trip (which Dean has no idea of the danger, but asked that of Cas anyway, just like he did at S4 finale, basically asking Cas to sacrifice for him and Cas just did; that's a whole topic for another day). So what if, as soon as they landed and Dean found Cas lying on the ground and bleeding out, Cas is actually looking like he's really going to die right then and there, blue light in the mouth and eyes kind of a life-threatening situation, grace flying out of the body, and Dean panicks and has to act quickly and the only thing he can think of to save his friend (which would also be ensuring the only way they know how to go back to their own timeline) is to let Cas go into him before they figure out what to do, possess him, use Dean as a vessel, so Dean just says yes to Cas without much thinking. It's so easy to say yes to Cas. And voila, reveal that it's actually not really Cas; it's Michael pretending to be Cas (the real Cas is probably bloody wounded somewhere else nearby). By giving himself up for Cas, Dean essentially accidentally said yes to Michael, and Apocalypse 1.0, off we go.
(And then of course, just like every season, we'd have to fix this major catastrophic problem, and Cas and Sam and Bobby would save Dean back and try to stop the Apocalypse, and there's also still Lucifer hovering around Sam problem that needs solving. At the end of the day, I'd imagine just like Swan Song Sam struggling but winning over Lucifer, taking back control of his body using the memories, Dean would have gained a surge of strength from those he loves and takes back control (like, maybe Lucifer tortures Cas in front of Michael, and Dean gets so emotional/worried/furious that he fights his way out and uses Michael's power to blow Lucifer away to save Cas) and hopefully not end up jumping into the Hole. But if he did, and imagine it's Swan Song reversed, Lucifer jumps into the Hole with him (probably in Nick's vessel, or maybe in Adam? Since, well, he's a Winchester but they never say which one he's a substitute for, maybe he can be both Michael and Lucifer's vessel, so maybe when Lucifer realizes he just can't make Sam succumb, he'd trick and jump Adam instead), it would be Michael!Dean and Lucifer!Adam in the Hole, and guess what, we're damn sure that Cas would go down there and "lift him from perdition" again immediately after, like, just in at most a few days, and one hundred percent he wouldn't have left Dean's soul behind because he'd check so very carefully. Or if for whatever reason he couldn't manage that on the first try of rescue, he'd surely jump right back in to scoop his soul out on the second try. So, then, problem solved again, Apocalypse stopped, Michael/Lucifer in the Hole (sorry about Adam again), Dean/Cas alive, Sam/Bobby okay, yay happily ever after (Not really, there's still Raphael, but at least they'd work on it together now, without Dean's gap year of normal life, Cas wouldn't go to ally with Crowley, then there wouldn't be godstiel, which is what I considered the true point-of-no-return in the whole story, so at least this version, things wouldn't be as bad, I hope). Hopeful ending, then, which usually should be good enough.)