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I think there's a flaw in looking for *A* reason why uber-talented players are still relagated to the minors for a time, (even if it may just be for a cup of coffee).  I think there are a lot of little reasons - none by itself that would warrant the choice in cases like Junior or Horner or Strasburg, (et al) -- but taken as a whole, they probably do more good than harm.
First off -- not every college kid (and certainly not high school kids) -- has the same base in baseball fundamentals.  Oh, for sure if you attend one of the MLB player factories like Texas or almost any division one school in Florida - you're probably well grounded in fundamentals.  Basically, I think one of the reasons for the AA-detour is to prevent a kid from doing something egregiously stupid on the BIG state of MLB.  (The clubs are likely attempting to save themselves embarassment as much as the kid - but that only strengthens the argument).
Some of it is likely getting a solid baseline.  While the knee jerk is to assume that all the best personnel travel with the big club -- but I don't believe this is true.  The minors are where you put your best TEACHERS.  The majors, where you're typically dealing with finished products - you're more apt to have guys good at maintanence - rather than design and implementation.  You need to get as good a picture as you can with what you're dealing with - and look for any (previously) unseen problem areas. 
But, even if you've heavily scouted a player - there's nothing like eyes-on study to identify potential problem areas.  And - it is better to do this in an environment where winning is not the PRIMARY concern.  This is the huge diff between majors and minors.  Even Pittsburgh and KC are TRYING to win 90.  In the majors, you don't typically take a reliever and say -- "We're gonna start you tomorrow - let you go three innings - and just see how it works out."  And IMO, there is humongous danger in thinking you can take such an approach with one guy - just for a little while.  I think that could undermine the entire concept that you're actually interested in winning anything for the whole season.
Some of it is simple ego-management.  Give a kid a little taste of the minors, and maybe he appreciates exactly how special the majors actually are.  Remember that this is all dealing with kids from 17 to 21.  Most of these kids have never held a job of any kind, or had any significant amount of money of their own. 
Ultimately - I suspect that the AA two-step is a good thing - mostly driven by the fact that these kids - regardless of talent level - are still kids.  And while there is nothing to be gained in sending your strat-o-matic card to Durham for a month -- there may be a lot of HUMAN plusses to sending Joe Bob.  Just like almost any job in America -- there is some form of orientation -- where the new hire must deal with a bunch of stuff that has nothing to do with his actual job.