So let's say: restart the whole idea of a multiverse - wall it off and consider that a done-deal.
That seems to be the most likely option with the most Pros. The Cons will be in regards to the lack of consequences and basically doing what the comics did to maintain (no pun intended) shelf-life...However, the MCU is not eternal nor able to sustain that same lifespan as the comics have and still do after 80+ years. With no consequences cinematically, you've proven the criticisms regarding "lack of stakes" right from the average movie-going audience and those who are sick of the MCU. The stakes presented in Secret Wars will not matter by the end if the multiverse is restored and never acknowledged ever again; so what stops our heroes from venturing to another Earth again someday or another interruption or outside force from another Earth?
Then we're back to square one. "Multiverse Saga Part 2". This isn't the comics, we're dealing with a shared universe divided into Sagas and a large overall storyline that will eventually have an ending.
BUT if the multiverse collapses, timelines or specific elements converge and become one - you have exceeded the expectations by proving there ARE lasting consequences and the stakes were legit...but you lose all these beloved universes of yesteryear like Sam Raimi's Spider-Man and the X-Men film universe. They're all dead now.
Worse, you got more homework to do. What's gone forever and what's merged? Stuff like Raimi's Spider-Man's timeline cannot merge with the MCU's for obvious reasons. What domino effects are created as a result of the F4 and mutants existing for decades? The Sokovia Accords and Agents of SHIELD wouldn't happen now because gifted individuals were presented as a rare phenomenon. Then you have to answer more questions like what's canon and what's not? These are going to have be acknowledged and not scattered puzzle pieces we have to think over and piece together ourselves, like the Arrowverse and its adjacent material expected us to do. That's bullshit. The MCU would die from asking too much from casual fans by that point or Feige would have to break his promise about "no more homework" for Marvel Studios continuity consultants.
What about character traits so specific they won't work with these outside elements? For example, Nico Minoru's mom being dead in Your Friendly Neighborhood Spider-Man being undone erases her whole story-arc in that show if elements from that series carry over into a hypothetical merged timeline. But if it remains intact, you've erased the events of Runaways.
I think I would prefer the latter, but that would mean AoS and Runaways specifically are just wiped from canon entirely post-Secret Wars. Quake can still exist, but her origin just occurs some other way. All in all, I think Marvel has to be discussing this right now. They need to.
I don't think the "reset" is actually going to merge everything like Raimi, YFNSM, etc. or kill those universes.
I saw the whole "return to singular timeline" thing as returning to focusing on a single universe instead of multiverse plots, meaning Raimi and TASM's stories are ending in the sense that they won't play into anymore MCU stories, but they still exist. It'd be no different from if No Way Home didn't bring them back. Their universes still exist but we won't be seeing them. And I 100% doubt that YFNSM is going to supplant what they already have with MCU Spider-Man
The thing stopping the heroes from going to another Earth/interacting with another one and Multiverse Saga part 2 is…not writing something where the multiverse comes up.
I would bet my soul that a Fantastic Four sequel will deal with the repercussions their existence has had on the universe and their place in it. Stuff like not forming in the 60's and the lack of 828 optimism, them being present during the events of Infinity War (and nothing actually changing lmao), and the overall conflict of existing in a world with over a hundred more heroes and villains.
As for the X-Men I doubt the FOXverse will be treated as a merge in the same way the F4 would be. Feige said the plan is for the X-Men to be more of an adolescent team than an established one, like FOX had them. That'd already disqualify most of what could be carried over from the FOX universe. Younger X-Men would also somewhat mitigate the issue you brought up of AoS treating enhanced individuals as relatively rare. Public knowledge of Mutants, X-Men, and the X-Gene would be treated as something relatively new rather than something that played a significant role in the Infinity Saga.
Their mark on history would be things like Steve fighting alongside Logan (played by 88 year old Hugh Jackman) during WWII and everyone calling him Lucky Jim because he was super "lucky" and never seemed to get killed.
I don't think a "reset" and merge like I outlined would be super invasive. I think them going all in and trying to make a new universe while trying to keep big chunks of the old is what would be a problem. Folding their F4 and Mutants into what they already have is far safer imo.
I also think using this as an excuse to recast/bring back characters can work if they treat it as them coming back to life (either resurrection or variants like Gamora), rather than rewriting history so that they didn't die, bc that'll have consequences I don't trust them to address.
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