Personally, my ideal scenario for an E4 challenge is a sort of middle ground between the two; the members can be challenged in any order, but their Pokémon all increase by 1 level for each member defeated. Basically if they start out with levels of, say, (50, 50, 50, 50, 52), then after you defeat the one whichever of the remaining three has levels of (51, 51, 51, 51, 53). It gives the increasing challenge of the linear-order E4s, but less so, and it gives the flexibility of the any-order E4s with less opportunity to steamroll the last member faced.
Though a related thing I’ve had issue with is the tendency to have major teams be “all Pokémon at a certain level except the ace which is two levels higher”. It just feels stale, not to mention unnatural… on that note, my example above could be better as something like (50, 51, 51, 52, 53) and so on.