I agree with you. I had read at least one comment that said "it's a waste of time" and I always cringe at those words. :)
I also think some places need time to really appreciate. I had enough time at NF that first trip so that I could spend some time just watching the water pouring over the edge - a half day wouldn't have allowed for that at all. Just experiencing that was enough to turn a "tacky tourist trap" into an amazing place. This was mentioned by several on a thread about how much time was needed in Yellowstone - you can do a flyby hit of all the high-points, but to really get Yellowstone, you need to give it time to sink in.
I totally agree about the driving, especially the SD to Yosemite. And I agree, it might be best to skip SD because of that due to the pace of the trip in general. However, it could also be argued to skip something else and spend more time in SD so that the drive to Yosemite isn't as big an issue. It's up to the OP to determine which places are non-negotiable.