Because you'd invariably fuck shit up if you did that.
Superman's the son of Jor-El, sent from Krypton when it blowed up, raised by the Kents in Smallville, works for the Daily Planet in Metropolis, and wants to break Lois Lane in half with his super-cock. This is all set in stone. You can't change it. Ever.
Whether Brainiac blew up Krypton, whether Clark Kent ever had a Kryptonian dog when he was a kid, whether there's another chick with an oddly similar name that Superman wants to bang - these are variables. You can accept or ignore them. Just set it as a ground rule in the beginning that you're recognizing THIS continuity and you're good to go.
A full-on reset would require that you either change the base - which is BAD and WRONG and you will not get away with it - or write the base again, which is boring. Thad's right, you almost have to ignore bits of continuity in order to write a workable story, but that's as far as you can go.
Of course this brings us back to Wonder Woman - what's her base? She has some sort of hazy connection to Greek mythology, and she's got some pretty goofy powers that are well-known but hardly necessary. There isn't anything about her that you can't change without screwing it up. Wonder Woman being just another powerful Amazon woman who wandered out of her tribe with no connection to mythology whatsoever? Sure (although you might need to explain why she's so white). Wonder Woman without the bullet-deflecting bracelets, or the truth lasso, or the invisible airplane? That's all silly, you can get rid of that. Wonder Woman without the sloganized bra and star-studded underpants? Sure, go ahead. She may as well be a really strong blonde chick in street clothes. Or a bitchy woman in a french maid costume who fights with her shoes.