Exactly. Can you imagine tuning into your favourite TV show mid-season, but the writers have decided to change some stuff, but not other stuff , and the story is "already in progress". WTH?
To be fair, that has also happened...
The problem I see with this isn't the storytelling problem. I can figure out the new status quo quickly enough, and I'm sure any reader who cares can, too, especially with fans hammering it out on the Internet.
My problem is that it shows a lack of professionalism. "Everything is new without the shackles of continuity...except for Blackest Night (and a hundred or so other stories), because we all agreed that story was wicked cool!!" It makes them as easy to take seriously as the woman I met once who explained that she was a strict vegetarian, except that she had bacon every day.
I think the problem wasn't with Crisis (although is was unnecessary), its that they didn't take that opportunity to restart all their story-telling. If I were running a shared universe superhero comic book company (yeah, right), I'd likely restart everything every 25 years or so.
Well, the goal of Crisis notwithstanding, they weren't trying to mainstream comics at that point, and they didn't want to kill off the top-selling books like New Teen Titans. Really, if you think about it, the new DC Universe then was created entirely to support that ecosystem, in a way, except somehow for Wonder Woman.
And, of course, the actual goal of Crisis wasn't really to clean up history. I forget the exact issue number, but there's an old Green Lantern letter column where a fan takes the writers to task (jokingly) for having Hal not recognize...oh, some space hero, when the two met in Showcase #100 where every previous Showcase star participated.
The response (by Marv Wolfman) berates the guy for taking that other story seriously, explaining that it couldn't possibly have happened in the "canon" DCU because it included characters like Binky. Apparently, teenagers without powers (or angst) should exist in Marv's version of comics, and he mentions that he has a master plan for getting DC to outline what is and is not part of the "DC canon."
So that's what Crisis was for: Killing Binky and His Buddies. Over time, it changed to paring down the Infinite Earths to finite Earths (1, 2, S, X, and sometimes 4), then became a unified history and reboot...except for the popular franchises, and with miscommunication about what, exactly, that meant, over the course of the year's publishing.
My thinking is that DC, especially, should be handled the way the main characters were handled during the transition between Golden and Silver Ages: When you make changes and find a status quo that's popular, then...what, no, Kryptonians were never super while they were on Krypton.
Eliminate the old version from all the new books, and move forward from there, without wondering how this changes other characters.
I suspect that's what was happening in the late '60s, actually. Martian Manhunter becomes a superspy, Wonder Woman becomes a martial artist fashion plate, Superman loses some of his powers, and so forth. Had they not bailed on every single change, I have a feeling each of them would've gotten new origins by 1972 or so, and just pushed on.