In my opinion I think the 3 hour waits are mostly caused by the Genie + system and the ratio of Lightning lane VS. standby folks getting on an attraction.
Priority is heavily weighted to LL folks while only a few at a time are let on from standby.
Now that folks are paying for LL Disney really has no choice but to do this.
When FastPasses were free, it didn’t matter as much.
I think, since it was free, there was not so much pressure for the cast members get all the fast pass folks through the line and the ratio wasn’t so slanted.
I remember the good old days of paper Fastpass when I we would go to the end of the standby of an attraction and give folks our FastPasses.
It was a free way to spend some surprise Magic to a random guests at no cost to you.