I think Disney is in a "damned if you do, damned if you don't".
Option 1 (ECVs load first): The good part of this is there's fewer people on the bus, therefore making it easier to load and secure the
ECV. The bad part of this is the ECV group could "jump"/"cut" the line of people who have been waiting already, possibly causing THOSE groups to split (or the whole group to wait for another bus). To my knowledge, there's really no way for a driver to know if the ECV pulled up a minute before he arrived or 15.
Option 2 (ECVs load in order they get there): The good thing is this appears "fair" to other guests already in line. The bad thing is a loaded bus would be more difficult/unsafe to load and secure an ECV, possibly even forcing people to get up from their seats and stand for the ride (I believe there are seats that can be used if an ECV is NOT on the bus).
For anyone who gets upset ECVs load first, just remember "there but for the grace of God go I". If you REALLY think the ECV person (and their group) is "getting one over on you", think about whether you'd like to be confined to an ECV for a Disney trip.