Could troop loading be changed such that the speed of loading for a fleet is the sum of the capabilities of the ships in the fleet? As far as I can tell, right now a fleet of ships with troop transports loads one unit into one ship, then the next unit in the next ship, i.e. all serially, when it really should be one unit at a time PER SHIP, i.e. ships can load troops in parallel, or at least the fleet loading speed should act as if that's what's happening. This would make boarding fighters a lot, lot less micro-intensive when you need your troops back on board asap.
If this is already happening, feel free to correct me, but I don't believe that's the case based on my tests.