I don't mind having books about events in the standard continuity. But having them be central? That's the metaplot problem writ large.
I mean, I've already *read* the Civil War line. I know what happens. Why would I want to play through it?
If my play matches the standard continuity, there wasn't much point to the exercise, so to speak.
If my play doesn't match, then I have a problem for the future - what I have in my game will no longer match the next set of books to come out.
I would much prefer a stand-alone core, with supplements for those who want them
I seem to remember the Secret Wars module in TSR's old MSH rpg to be good fun, despite being exactly the same strategy. No one seemed to care that we had all read it, or that our Secret Wars turned out differently.
The one thing that has always somewhat bothered me about Marvel (and DC) RPGs is that they seem to push using their heroes instead of your own*.
. Otherwise, you might as well just be playing Mutants and Masterminds.

(Dungeons & Dragons)
Rulebook featuring "high magic" options, including a host of new spells.