Instead of saying that your daughter can't walk, it might have been better to explain that your daughter couldn't transfer from the wheelchair. On rides like Little Mermaid, it might have made more sense to the CMs to say that she needs your assistance to transfer, so she needs the moving walkway stopped. Just saying that she can't walk, had ankle surgery or has bone pain doesn't adequately describe her mobility issue. Also, instead of going to guest services and coming back later, did you try asking for a ride lead?
On Space, from the FP return there is still quite a long queue, so I'd say a 20 minute wait isn't totally out of line. I'd rather have a FP to come back to the HA entrance than wait in that little alcove and inch the wheelchair forward for an hour or longer.
On HM, there is a separate HA entrance. I've never seen a wheelchair in the regular queue. If you waited in the regular queue without asking a CM first, that's not on Disney. There is a limit for how many non-ambulatory guests can ride due to evacuation procedures. Also, their goal is to only stop the ride once per cycle. I don't know that they succeed there, as it seems to stop 2-3 times per ride every time I ride. And honestly, once I don't mind, but 3 times is pretty annoying. I appreciate that they try to load and unload wheelchairs at the same time to keep the ride moving. I have 3 friends in wheelchairs, two can transfer and one can't. One who can transfer uses a wheelchair full time, one only at DL due to ankle surgery. (I've never been with 2 of them at the same time.) The one who can transfer chooses not to use the wheelchair on HM, the one who can't will do HMH first thing in the morning, when the HA wait is shorter. My friend who can't transfer from the chair is an AP, and plans visits in a way that takes into account wait time and procedures at HA queues.
As far as the wait on Jungle Cruise, there is only 1 boat that can accommodate a wheelchair, it takes as long as it takes to make a circuit. The HA waiting area is not that big, so it makes sense that they would try to keep it clear so wheelchair users who can transfer can get through. It may seem frustrating, but at least they have a dedicated ride vehicle, when many rides don't.