Hans Cholder mentions an airline that I am intimately familiar with.
The reason the -200 aircraft are operated as a single type is simply a matter of cost and managerial acumen. In order to integrate the other Boeings with the -200 a Side Letter of Agreement to the Collective Bargaining Agreement would be required. There are several problems with this. One problem is that any integration would inherantly provide efficiencies to the operation. A portion of these efficiencies would have to passed on to the entire pilot group through a quid pro qou. This particular airline hates to return anything to the pilot group. Another problem is that this agreement would probably require membership ratification of the Side Letter. Under the current atmosphere of pilot anger with management this would probably fail miserably. This Side Letter would probably have certain work rule restrictions that would tie the Company's hands to a certain extent. This Company hates to have to comply with these types of restrictions. Or to put it another way- if grown ups ran the airline there would have long ago been an integration of the -200 and the other Boeings and the operation would be more efficient.
As for the -900. It is currently built into the lines time for June. The only training that a 737-4/7/9 pilot will receive regarding the -900 is a training handout.
Continental has operated the -100, -200, and all their other 737's as a single type. There was recently a very good article regarding this in either Airline or Airliners magazine.