Crisis wasn’t focused to much on fixing inconsistencies as it was on reducing complexity by reducing the myriad dimensions of the multiverse to a single universe. I suspect they planned to fix problems at the same time, but they’re still cleaning up the inconsistencies *created* by the Crisis.
Let’s look at the Titans (since I’ve been reading them since 1984). Since Wonder Woman hadn’t appeared yet in the post-Crisis universe, Wonder Girl couldn’t be her adopted sister, so she needed a new origin. A few months before the Crisis, they had finally revealed the origin of an early Titans character, Lilith, in a story involving the mythical Greek Titans. The new origin they came up with for Wonder Girl *contradicted* the origin they had just written for Lilith! Not only that, but the Lilith origin had introduced a group of villains called the Children of the Sun, so *they* needed a new origin too! And this is just one writer (Marv Wolfman co-wrote Crisis and wrote Titans from about 1980-1994).
Probably the most infamous contradictions were the result of erasing Superboy despite his key position in Legion of Superheroes history. They were trying to fix that one for years with one patch after another until they started over with Zero Hour.
Now Zero Hour, despite being (in my opinion) the far inferior story of the two, was definitely intended to clean up inconsistencies. It didn’t (at least, not much). Except for the Legion, I don’t think much of anything *really* changed as a result of Zero Hour.
I guess that’s part of why Waid and Morrison came up with the overlapping part of Hypertime: to acknowledge that inconsistencies exist.
And I hate to say this, because I really like the way Geoff Johns has been handling the Flash, but glaring inconsistencies keep popping up (Goldface shouldn’t be that old, and since he’s a cop killer he shouldn’t be out yet and the cops should hate his guts, Iris couldn’t have been around when Julie was pregnant unless she was time travelling more than we know, Chillblaine wasn’t “found” dead, Polaris flat-out killed him, etc. – although that last bit I need to check up on to see if I remember it correctly).
Anyway, there’s an interesting story on how long it took for the changes made in the Crisis to really stick in the introduction to “Legend of the Green Flame,” Neil Gaiman’s Superman/Green Lantern story which didn’t get printed for a decade. Apparently there was major disagreement among the editors as to just what had changed or was going to change. As whoever was writing the intro put it: (and I’m paraphrasing here) “on Mondays, Wednesdays and Fridays, Green Lantern knew Superman was Clark Kent. Neil’s story was written on a Wednesday, but turned in on a Thursday.” Since it hinged on there being a friendship between Supes and GL, they axed the story.