I want to quickly chime in, but be warned that I'm not considering any sort of scanner rights. I love you guys and want people to respect your wishes, but at least in the United States, there's no copyright on scans. So please be patient with people who want to mess with'em, since they're allowed.
Purely from a reader standpoint, I'd also prefer the scans as raw as possible. Repairs are fine, but I feel that any "enhancements" invariably try to make the comics into something...false. We can argue whether it's better until the cows come home (and then ask the cows their opinion), but to me, the more you change the original image from what was scanned, the more it becomes the editor's art than the artist's.
It's worth noting that serious "upgrades" introduce a new wrinkle: Legally, it puts us in a gray area. The UK considers some sorts of mechanical reproduction as worthy of copyright (though a collection or collage/remix does not--go figure). It sounds stupid, but we all know of stupid lawsuits of heirs coming out of the woodwork to get some cash: Someone's trying to lay claim to some of Charles Babbage's personal papers!
On a technical level (Snard hints at this), also don't forget that every change you make (even just innocently rotating the scan, not that I don't want anybody doing it...) is a net loss of information. If it were to replace the original, that's an irreversible change, which is never a good idea. It's like magnifying a small image--you'll get really big pixels, but not a better image.
I think of color like advertising: Most people ignore it, but a few people are interested in only that aspect. If, in five years, someone wants to study the paper or ink in Golden Age books, it's more difficult by having pages that try to hide the paper and change the color of the ink. And like removing ads, it's infinitely easier for a user who doesn't like it to change the colors than change them back.
The discussion is getting pretty heavily stacked, here, though. Can someone who likes the edited versions explain the benefits? "I like the bright colors" is acceptable to me. It occurred to me while typing this that I can't think of a single reason to prefer editing and am really curious why it's a popular idea.