To be fair, baseball isn't fully funded, so any state with a large population base is going to have advantages because they have a larger pool of in-state players for whom in-state tuition can be paid (when you're on a quarter or a half of a scholarship, paying out of state tuition adds up real quick). To me, that is a much larger issue than the seasonality of north vs. south teams - if baseball was fully funded (20ish full scholarships) then that discrepancy would go away pretty fast.
That said, as others have pointed out, we need to drop the loser mentality and making NCAAs every other year or one out of every three years is completely attainable with a competent head coach (and, the same is true of every Olympic sport we have).