I think that ultimately the problem is that monorails are a lot more expensive to build and operate than a fleet of buses, and are far less flexible as "people movers". They're a great attraction or "ride" but WDW is unfortunately saddled with a lot more monorail track than is necessary just to provide a fun ride.
Buses are really boring and ordinary, but there's nothing to beat them in terms of simplicity of building, maintaining and operating them. Buses go literally anywhere you want except across water. You can put extra buses on easily, change their routes or send them on a detour as easily as sending a 5 second radio message to the driver.
Every mile of monorail track that you build must cost at least 50 or 100 times more than building a mile of asphalt roadway for buses. Although each monorail train carries more people than a bus, the nature of the beast is such that lots of control, supervision and maintenance people must be involved in watching and directing the trains. Not to mention a lot of computers, software, monitoring and signalling systems.
There are many suppliers of buses, every year new and better models are available, replacement parts are plentiful, and there are tens of thousands of people out there who are capable of operating and fixing buses with very little extra training required.
Monorails are a completely unique, custom piece of equipment with no ready suppliers at all, so procuring them is an extremely complicated and lengthy process. There is no aftermarket whatsoever for vehicles or parts.
If a bus breaks down, it rolls to the side of the road, another bus picks up the stranded passengers within minutes, and all the other buses continue to use the road as if nothing happened.
You can't re-route a monorail, and if one train has the slightest glitch, the entire track is blocked until the train can be fixed or towed away, and usually the "towing away" requires the shutdown of some of the other monorail tracks in order to move the train to the sheds. Passengers can't be evacuated without an elaborate and dangerous procedure involving ladders, etc.
It's a completely unique vehicle so you can't put out an ad for a trained and experienced monorail engineer or driver (err, pilot). You have to do 100% of the training yourself, as well as developing all of the required standards and procedures for operation and maintenance.
So although they're a really, really cool and fun attraction, monorails just aren't the practical form of transportation that Walt imagined. It looks really bad when Disney shuts down or scales back the monorails, or neglects the little cleaning and maintenance jobs mentioned in the linked article, but in this case I sympathize with them for pinching pennies.
Possibly a good long-term solution would be to simplify the track layout so that there is only a single route which circles the lagoon then loops down to Epcot and back. It wouldn't be as easy to use them as transportation to get between resorts/TTC and magic kingdom, but as explained above, they're pretty poor as "people movers" anyways. So by simplifying the tracks you could still operate them for the "gee whiz" factor and spare a lot of the huge expense of operating 3 different tracks with 3 different sets of trains.