First of all, Disney was working on changing the system long before there were those news stories about people hiring folks with a GAC. The real problem is that the GAC system was designed with a lot fewer users in mind, and so it got overwhelmed.
Second, I believe that Disney, if there is a long kiosk line, will take that waiting time into account. If the line looks long, keep track of how long you were in the queue.
Third, the app that Disney is using to judge wait times is free to the public as well - so you can know what the wait time is before even getting in the kiosk line. I asked Disney how they would handle the kiosk lines getting long, and they said they were aware and addressing it. That being said, do not go to get in the kiosk line right after a parade, fireworks, Fantasmic, etc.
About the wait times being inaccurate - that is one reason I will be looking at more than the Disney app. If I see a major discrepancy, I will either ask them about it, or ride a different attraction.
When you wait your 90 minutes, using your example, and then show up to the ride and see a 45 minute posted wait, that does not mean you have waited an incorrect amount of time - that just means that the wait time when you got the Return Time was 90 minutes, and then an hour and a half later, it may be shorter. And yes, I am sure there is a time that the posted wait time reported to the kiosk is incorrect - no one is perfect. But in general, I have found the posted time to be nearly always correct. And don't forget, there will be times that you get a Return Time for 45 minutes and it turns out that the wait time was incorrect, it was actually 90! Just remember that it can go both ways, and I am sure that if you wait a shorter time than actual stand-by, you would not want them penalizing you on your next ride!
When it comes to things to do that do not have a wait, here is a partial list...
There are plenty of things to do in Disneyland that either require no wait or have short waits. There is
Mickey and the Magical Map (the theatre seats 1800 - I have never seen it full),
Tiki Room (continuous shows),
Billy Hill and the Hillbillies (generally 4-5 shows/day, no lines beforehand - just go in),
Fantasy Faire Royal Theatre (8 shows a day),
Laughing Stock, ride the
Mark Twain and/or the
Columbia (yes, this wait area can be crowded, but tell the CM letting you in that your son is autistic, can they give you a place to the side - I do this now),
Dapper Dans,
Main Street Marching Band,
Firehouse band, Straw Hatters, Pearl-Something Band, Boot Strappers, Jazz in New Orleans Square, coloring in Big Thunder Ranch jamboree,
seeing/petting the animals in Big Thunder Ranch,
Main Street vehicles (horse drawn trolley, fire truck, car, and bus),
Mickey's House,
Minnie's House,
Chip and Dale Treehouse,
Tarzan's Treehouse, all the buttons and things to touch in
Toontown outside Roger Rabbit,
Tom Sawyer Island (which has both places to play and quiet corners),
Disneyland Railroad (which generally is not going to have a wait),
Ragtime Piano Player (Coke Corner),
Innoventions,
Capt Eo,
Main Street Theatre (with black and white Mickey cartoons),
Disney Gallery with the 50th anniversary video playing,
Great Moments with Mr. Lincoln,
Jedi Training Academy...
All of this I came up with off the top of my head. I am in a wheelchair, cannot handle crowds, have ADHD in addition to other things, and I rarely transfer, so that means I look at all the things I listed above, often. I rarely actually enter an "attraction." I will start compiling a list for families like yours who may not know about these things. I will also make one for DCA. Tonight I am too tired to write it all down, but this is just what I came up with off the top of my head. There is a lot to enjoy, in both parks.
I, too, understand about how this waiting system can be unfair, as I usually need to wait for a wheelchair accessible vehicle (WAV) or transfer accessible vehicle (TAV). This means that after I wait my turn, with the
DAS (assuming I get one), I am going to have to wait again for the WAV or TAV. I may also need to wait because there is a limit to the number of wheelchair users allowed on an attraction at any one time. This means if three wheelchair users all show up at Casey Junior Circus Train at the same time, even if we have waiting the appropriate stand-by time, I get to wait for the entire ride to cycle 3 times. So I fully understand about how the system is not perfect, but no system is. The GAC system certainly is not (otherwise I would not wait twice as long in the heat and sun to get on Pirates!)
Keep an eye here for more information about what you can do that does not require waiting - there are more shows than you think!