It is NOT cost effective for three or four empty Epcot buses to come and go from a hotel in a row while people wait 30-45 minutes for one to the Magic Kingdom -- and I've seen this happen more than once (not always for Epcot/MK, but you get the idea).
No, those instances aren't.
But you're looking at (potentially) aberrations within a complete system. As long as the aberrations are relatively few and far between, the cost effectiveness lost from them isn't outweighed by the cost effectiveness of the system as a whole, especially when taking into account sheer volume.
A good example is mass production. Every mass production line has an inherent error rate. If you're sitting there watching the "bad" bottles get kicked out during quality testing....you're going to be SHOCKED at the number of bottles being dropped off the line. The sheer volume seems astounding. But when you take into account that a line can see 500k to 1 million bottles per day make it past QC...suddenly you realize that the aberrations are miniscule compared to the cost benefit and sheer volume being kicked out.
I suspect (though, as is the case for all these discussions on the Diz...it's all theorycrafting) that's what the Disney execs would say to you in a moment of weakness. No system is perfect (remember "The Matrix"!). So it comes down to this: Is the system successful enough to meet it's goals (in this case: to transport hotel guests to the theme parks), efficient enough to not create too much customer (guest) DIS-satisfaction, while balancing overall cost to the company (and make no mistake...when balancing cost to efficiency...cost carries a bit more weight).
I'm not going to sit here and say, categorically, that the current transportation system does that. I don't know. What I do know is that Disney, when it comes to data, seems like they'd fit right in on the show "Hoarders". They seem to collect an AWFUL lot of it...which makes me think they use it (because otherwise...why bother). And, in their minds, this seems to be the best system they can come up with right now.
I have my own quibbles (like you do) with that system, for sure. And I've seen anecdotal aberrations, too (just like you mention above). It certainly doesn't meet all MY needs, at the resort.
But if we're going to talk about the business, we have to try to "think" like a business does...not like a guest. And from what I've seen...I think Disney's version of public transportation is probably about as efficient as they can make it, it is tolerable to most guests (as in, it doesn't kill their Guest Satisfaction ratings, overall), and it's as cost efficient as they can make it. In other words: Unless some cheaper, more efficient tech comes around that ALSO improves guest satisfaction ratings....I think this is probably what Disney's going to stick with for awhile. They might make improvements (I hope they do), given new efficiency models, more data, or new tech...but I doubt the overall system changes until we can say "Beam me up, Mickey" or they take a page from Logan's Run.