I think its more than just refurbing the trains. The trains are just part of a much larger system.
They would have to bring down the entire system or at least an entire rail.
And yes doing this may lessen the frequency of these brake downs but it won't stop them.
Oh yeah, I know. When I used to work on the Monorails, at least one train a day would just die somewhere on the track, so the tractor would have to come out and tow it to the station. It's such a hassle.
likewise for the bathroom situation usually whenever I stop at one there's a bathroom attendant near by or inside the bathroom. 

finding a clean restroom at WDW than I do at other parks. Sometimes they're not in great shape, but usually they're tolerable. 

