icarus- Always keep in mind that the parks are a business and they are expected to make profits. There were several reasons the subs closed in Disneyland- and they all became a problem at about the same time...
First, new laws regarding pollution emisions came into effect. The subs were deisel powered and had no modern pollutant reduction systems. Plus they were costly to operate and there was no way to retrofit other cleaner power plants.
Probably the biggest factor though was a law that was, I think from Orange County, that when attractions underwent a major rehab, the new version had to comply with then recent laws regarding equal access for persons with disabilities. There was no way a wheel chair was going down the steps of the subs, and at the time, no one wanted to commit to making an investment of the needed magnitude to make the attraction compliant with all the new ordinances. Budgets for park attractions were being slashed, even for those already under construction. It was more important that the top exec to make an absurd bonus.
I do not know why the subs in WDW were closed, but I would guess the contributing factors were similar to the ones in DL.
The Skyway had similar problems. To work smoothly, Skyway needed to run continuously. Stopping the cables presented mechanical problems, so as the new laws came into effect in regards to people with disablities, everyone realized that this "ride" was not one that would be able to be stopped every so often for disabled access.
But an even more serious problem that received almost NO public press was the issue of "projectiles". There had been many complaints about youths spitting from the gondolas. There had also been reports of people dropping things onto people below. A "reckless prank by a teen" could easily turn into a danger and further, into a liability if someone on the ground was struck by an object tossed from the sky.
You always hear that the Skyway was closed because a CM at WDW died when he held on to a gondola and fell to his death. However, although this excuse was spotlighted in the press, the decision to end the attraction had been made before this ever happened.
I'm sorry I don't remember more exact details, but the important thing to understand is that both these attractions were engineered and built in the 50's, and that was a totally different time. Laws change, park guests change, new mechanical technologies evolve, and attractions like these become dinosaurs.
Now... on to "Mr. Toads Wild Ride" at WDW! The attraction was based on the Disney short, "Wind in the Willows" which was a relatively minor Disney hit. Back then, there was a major push to make Winnie the Pooh, a bigger merchandise money maker than MICKEY MOUSE! I know, you are thinking I'm nuts, but I heard a top merchandise exec say it and she was even excited about it! Although very popular, W. T. Pooh never reached that plateau... but the kiddies know Pooh, they didn't know the "frog"! Although I have never seen the Pooh attraction, I have seen the lines! I'm guessing that was a good corporate decision...
I hope you now have a better understanding of what really happened. It's just a business...