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Because nobody was asking for it. COIE was literally the Charleton heroes' first appearance in the pages of DC Comics. They showed up just in time to be "incorporated" into the mainstream DC universe. You might as well ask why they didn't have Billy Batson jump Earths just so he could appear in Justice League stories. Or the Freedom Fighters, their own book took place on Earth-One, yet nobody thought to have any of them join the Justice League.
Writing about comics https://bookofhsssh.blogspot.com
People also need to remember that DC was in the toilet before Crisis. The only hit books they had were Teen Titans, Batman, and Legion. Everything else the sales sucked, and even Batman wasn't selling like he would in a few years after the first movie came out in 1989. As much damage as Crisis did do to some properties it probably saved DC as a whole from going under by bringing in a whole new generation of fans.
Buried Alien - THE FASTEST POST ALIVE!
First CBR Appearance (Historical): November, 1996
First CBR Appearance (Modern): April, 2014
In the real world i would be BOTH pro registration and Pro mutant rights. Xavier and Trask were both right.
I'm not going to pretend that I know what the "easy" answer was. Maybe rebooting truly was the only way. In recent years I've kind of leaned in that direction. BUT I also feel like they didn't try very hard in the years leading up to COIE to fix their books either. By the mid-seventies Spider Man was already engaged. Meanwhile Superman wasn't even allowed to let Lois in on his secret. Go back and look at the kinds of stories they were telling in the years leading up to COIE. Then go back and look at the kind of stories Marvel was telling. DC was still publishing super-baby stories well into the eighties! Not that I have a problem with the concept of super-baby but no one wanted to read stories about a toddler plugging up volcanoes in 1981. They could have tried a lot harder than they did and recognized that the audience was growing up.
Assassinate Putin!
Only actual "problem" caused by wiping the slate clean with Wonder Woman was the headache for Donna Troy fans over her origin. Which given Donna is a Titans character, I can see why she wasn't really factored into what do with a WW reboot.
Other than that, doing away with four decades of post-Marston mediocrity was a godsend for WW.
Continuity-wise, it's Crisis On Infinite Earths. The story and art are magnificent, but the "either/or" approach forever weakened the DCU. Every event since has been an attempt to change and/or undo COIE. Had an earlier event, say, Zero Hour or Infinite Crisis repaired the core areas of damaged continuity, things might be very different today. As of now, however, it's too late and COIE, even if it no longer "happened," is to blame.
As Jon Clark says above, TDKR did the most damage to Batman and to superhero comic book storytelling. It was always a "possible future," yet it's success led to Miller's characterization for Batman and Superman becoming more and more prevalent in comics and other media. It's a vastly-overrated story that is eclipsed by dozens of regular runs in Batman's long history. I'll also blame Watchmen for further popularizing the notion that superheroes only work for adult readers when they're deconstructed. Every nightmarish misstep in comics and film (Identity Crisis, Infinite Crisis, New 52, Nolanman, Snyder's garbage) in the last thirty plus years can be blamed on those two "masterpieces."
As for changes, I think the change COIE could and should have made was that the infinite Multiverse is still there while the focus going forward is on a true "New Earth." This would have meant a full reboot: no Robins, no teams, all new #1s except for Action and Detective. Those could have become anthology books. Even if COIE had just left a vastly reduced "local" Multiverse (say, the five Earths that were collapsed into Clutter Earth) the DCU would have been streamlined and strengthened such that no alterations would really be needed.