Same reason the computer doesn't automatically beam stun grenades to wherever intruders appear. Rule of Drama.
Voyagers case was unique though, I do agree that his personality wasn't brilliant for their circumstances but we saw the Doctor change and grow. In the AQ though, his bad personality doesn't seem like enough of a reason to pull all the EMH Mk1's out of action, when the EMH would normally only be being used in emergency/life or death situations. And wouldn't it be easier to rewrite a personality subroutine instead of redesigning a whole new EMH Mk2
I think they should have rewritten his personality so it was exactly like Captain Janeway and then also given him Captain Janeway's hair (season 5 hair preferably).
I wonder if the Mark one became an issue in the early days of the Dominion War when things were going badly for Starfleet. EMHs may have been used frequently in these days. It's possible a few ships used a Mark two or three for a while as replacements may take a while to arrive.