I would think that they didn't want to rely so heavily on the mobile emitter. They've said more than once that they weren't completely sure how it worked since it was so much more advanced than their technology. What if the power ran out on it, or it was damaged somehow. if he was only in the mobile emitter in that case he would be lost.
I still wonder about Voyager's entire medical staff being killed when the ship is pulled into the Delta Quadrant. Sickbays are usually mentioned as being in the most heavily protected part of the ship.
maybe he could handle a common cold...but would he be able to perform and advanced procedure on a human? would he be able to come up with a new kind of procedure like the Doctor did on numerous occasions? I would say not since he wasn't programmed for that.
voyager lost a lot of peole when they got pulled into the Delta Quadrant. And it's a small ship so it wouldn't have that many medical people on board anyway. Also I would guess since they were only going on a two week mission they didn't have a ful medical staff. Probably just one doctor and one nurse.
I don't see why he couldn't do an advanced procedure. The program is not only knowlegeable but intelligent and active. It doesn't just sit there mindlessly looking up answers from a database. re: developing new procedures, that's exactly what he helped the doctor to do. Perhaps he couldn't by himself, I dunno. But it seems pretty clear to me voyager had the capacity to at least create a backup doctor, even if not one with equal R&D capabilities.