Considering however the ME has to deal with traffic issues, a train suddenly has benefits that I don't see mentioned here.. Even without traffic a train would be able to make it to Disney World much quicker than the M.E., which in turn would make up for the extra transfer.
I'm not saying it solves all the problems and makes it a seemless experience, but I do think you are under selling it here and ignoring problems inherent to the ME.
The only train that included Walt Disney World in the proposals was the high speed rail line, which is a heavy rail. That type of rail would be scheduled. To make economic sense, the schedule would be set to maximize the number of passengers. Running it empty would only lose money. That's basically true to any rail line. They are expensive to operate.
As such, it wouldn't be a short wait at the airport. Best case scenario would be once per hour during the day. Your wait would be longer during at other times. Since you would still have to wait to board a resort-specific bus at the Walt Disney World station, the entire process would be much longer than what happens today.
The most economically beneficial way to connect a single point (the airport) many disparate points (all the resorts) is a bus rapid transit (BRT) system. BRT systems are buses that operate in their own dedicated (or semi-dedicated) lanes. The dedicated lane allows buses to bypass normal traffic most of the way. Once they arrive at Disney World, the buses exit onto "normal" roads to get to the final destination. That's the fastest method possible with the fewest number of transfers.
If Disney really wanted to improve the arrival/departure experience, they'd pay to have a BRT installed on State Road 417 and World Center Parkway/Epcot Center Drive. Doing that would solve the traffic issues. Of course, that would cost money to fix a problem for which most guests probably don't blame Disney.
BRT routes are cheaper to build and operate compared to light rail and heavy rail lines. It can be hard to get good averages, as project costs can vary greatly based on local conditions. Estimated costs to build: BRT is $20 million per mile; Light rail is $40-200 million per mile; Heavy rail is $250 million to $1 billion plus per mile. The average BRT line cost about $120/hour to run. Light rail clocks in at $230/hour. [Unfortunately, I can't find a well-sourced estimate on the cost per hour to run heavy rail.]
Finally, I think it's important to note that Disney never intended to directly spend any money on a rail line. They intended to donate land along the I-4 corridor for the Walt Disney World station. Additionally, I believe all of this was happening before Disney's Magical Express was operational. If the high speed rail line was built, I'm certainly Disney would have used it to their advantage. But as it currently stands, I don't see Disney spending money on a BRT line just to improve the arrival/departure experience. Doing that would be a major expense with little upside other than getting guests to their resort a few minutes earlier.
Sources:
https://www.thoughtco.com/bus-and-light-rail-costs-2798852
https://www.thoughtco.com/rail-transit-projects-costs-2798796
https://object.cato.org/sites/cato.org/files/pubs/pdf/pa750_web.pdf (note: pdf)
I also like watching Melvin, Buff, and Max carrying on during the country bears show. I'm weird like that. just can't get enough of the attention to detail that disney brings. 
