In particular, I've heard that maintenance and pilot training are big issues. If you've got half your pilots on the 737 and half on the A320, you're much less resilient to scheduling issues than having all of them on one or the other. Similarly, I believe maintenance facilities tend to be one or the other, so if you've got half your facilities for each, at the margins you're going to have more scheduling issues for maintenance.
There are economies of scale with anything to do with scheduling flexibility, and dividing like this essentially halves those economies of scale.