I agree that there is a "cobbled" sense to the transition. Although MS gave his notice fairly late in the season, he had been hinting at it for some time, but apparently the writers had not put a continguency plan in the works. There is a feeling throughout the first few eps of S6 as though the writers were of two minds as to what to do with JQ -- put him in everywhere or put him in as little as possible (ok, one ep he's out of because the lad was getting married -- even actors are allowed to have lives).
I'm really hoping to see a lot more character development, including some backstory, in the latter half of S6 (and in any potential S7). The other team members have had 5 seasons to show aspects of themselves and JQ has a lot of catching up.
The comparison with Ezri Dax is entirely appropriate, although having set up the Trill species from STNG through DS9 we could accept her prior knowledge as carried by the Dax symbiote. Similarly, in Doctor Who, throughout the various incarnations, each was different, but carried the knowledge and experience of the former doctors.
Jonas' problem is that he isn't a Trill nor a new incarnation of Daniel. We have no real knowledge of his prior life or why he should just fall into place the way he has. We've been told he is a "quick study" (ooh, that's handy), has memorized all of DJ's notes (nice, but that doesn't mean he knows what DJ knew, only what he wrote down), and is very observant, as well as scientifically, linguistically, and diplomatically gifted. All very nice.
The writers have "grafted" characteristics onto him to fit him into the team. Jonas is entirely pleasant and very familiar, which in itself is a problem He lacks Teal'c's "alien-ness" -- a quality that still sets Teal'c apart even in S6.
I think we should be seeing JQ as a 'diamond in the rough' -- something alien, but not uncomfortable. An evolution over time might lead to JM's "charismatic leader," but I don't see Jonas just naturally turning messianic in the little time there is left.
It would also mean that S.G.-1 is totally politically correct - one male, one female, one black, one gay 
