The problem is that we almost have to give the characters some kind of variable power levels, since that is how Marvel itself consistently treats them. Otherwise we end up with too much chain scaling from fighting objectively far more powerful characters.
I know this sounds like a leap...
But if scaling is a major problem with the verse, can't we just disregard it to a degree. If characters are so inconsistent with one another that it's a large problem for the verse, then the proper scaling chains should be applied.
Whether that means not many characters genuinely scale to one another or not, if we're scaling characters in general, then we arguably should scale them to most of the feats they perform.
If it's to the point where, for example, Spiderman tiers are somewhat consistently shown as contending with tier 5s, then obviously something needs to be done for both parties, but that should affect the entire verses rules equally, not just groups of heroes that generally compare, because that's all of Marvel, as you say.
Tl:dr
Basically I personally think we should separate most character from their scaling chains, or at least make their chains wider tier-wise (tier 5s may vary from moon to planet level for example, but a note on their profiles to help stop confusion)
This would allow us to use genuine feats that characters achieve on their own more commonly, which is where writers definitely intend for characters to be placed, and still have them at very least, somewhat comparable to each other, while still showing differences in power.