I think that all things considered, Disney Transport does a phenomenal job. Walt Disney World is larger than some cities here in the U.S., and has a matrix of roads, destinations and departure points, all of which need to be carefully monitored and serviced regularly. Needless to day, the infrastructure is huge! The fleets of buses, boats, monorails, and trams all work together to move hundreds of thousands of people a day to all corners of the property. And it does so with minimal delays and expeditiously; you don't spend hours on the bus going from the BoardWalk Inn & Villas to the Magic Kingdom.
When you think about it, every single one of it's modes of transportation are NOT outright profit-makers; Guests don't pay each time they board the bus or a tram (granted, this is offset in ticket prices and room rates). In fact, I would be willing to bet that Disney Transport has some of the largest amounts of red ink to be found in the lairs of Walt Disney World Accounting. This just goes to show how dedicated Walt Disney World is to getting people to and fro in a timely, happy fashion. And we all know that that's because happy guests with lots of time will spend money!
However, just because everything runs smoothly and efficiently most of the time (it would be crass to say that perfection is demanded, if not expected) does not mean there is not room for any improvement. First of all, I definitely would like to see the new Nova buses in use throughout the world to replace the prehistoric fleet. Keep a few as trainers and CM transports, but that's it. Next, I would replace/upgrade the ferries and Friendships as needed. Finally, when and only when the above conditions have been satisfactorily met, I would begin construction on a new monorail loop and perhaps also a new and much larger TTC that I'd locate somewhere in between Epcot and Animal Kingdom. Those are my ideas, nay, dreams. But who knows, maybe Disney will surprise us and follow through with some nice new Transport.