Well, that was just bad timing. As much as I think Crisis was a bad idea, I do think that period of the late 80s through mid 90s were probably DC's best years. And at the time, there was no reason to believe they'd ever do another big reboot like Crisis again. When Zero Hour happened, it seemed like a relatively minor thing as an excuse to fix some minor issues through retcons, not a huge, world changing event (except for the Legion, of course).
But that's also exactly why Crisis wasn't necessary.