Good point. The other day I was running to catch a monorail at the Contemporary. My friend and I ran the entire length of the train before we finally found a car we could get into. Often as you say, a compartment was half full but blocking the open door. One thing we noticed was with seats facing each other people stick their legs out and add one stroller to that mix and that compartment is done. Luckily there aren't many strollers at Disney (nod, nod, wink, wink)
By turning the center seats there would be less legs blocking the door and more places to roll the strollers. Plus now you if one door is blocked you could enter the next door and circle around to the empty spaces. So, unless you hire those Professional Japanese Passenger Stuffers, people will always tend to block doorways.