I never understood the issue with the EMH's personality. It's there to be used in an emergency, do you really care if he introduces himself and says please or would rather he got straight on with the job and fixed the hole in your face thanks to Starfleet's engineers not investing in some fuse breakers?!
if he was only used as a short term suppliment then I don't see an issue. But in Voyager's case when he's the only doctor and there all the time, then you'd want someone with a better bedside manner
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