Tried to post this last night, but hit the board downtime by 4 min...
Yep. Obviously, the wait times would only drop so far but you only have to look at the FP math to see why there's a problem now. If you have an attraction with 2000 people/hr capacity, to experience a 90 min wait, you need 3000 people willing to wait that long in the queue in front of you. And to maintain a 90 min wait, that flow of people has to be continuously that high. That's a lot of people. But then lets say you divert, as easywdw says up to 70% of the seats to "reservations" ie FP. Then as far as the standby line is concerned there are only 600 seats, so a 90 min line only needs 900 people per hour, continually. A heck of a lot easier to obtain than 3000.
And you could see this in practice when something would happen on a ride, like say Tower of Terror when operating one drop shaft vs two. The line can get out of control, quickly. Seats diverted to FP are no different than taking vehicles out of service, as far as the standby line is concerned. FP effectively turns high capacity attractions into low capacity ones like Dumbo or Peter Pan for anyone not holding a FP.
Wait times are only partially dependent on ride capacity, and partially dependent on the thought bubbles over people's heads ala Roller Coaster Tycoon. It seems like someone thought that it was a simple thing to move people out of a standby into a virtual queue, and if that is what really happens, things might be okay. In practice, the virtual queue is partially filled with a bunch of people who were never in the standby queue to begin with (which is WHY some people like it so much). In order to accommodate these "new" riders, somebody has to either lose their seat, or the wait time has to go up, since ride capacity hasn't changed.
So to take our 2000 people per hour ride. 1400 slots get distributed via FP, but lets say 30% of those are new riders. That means 420 are new, and therefore only 980 can move from standby to FP. So as far as standby people are concerned, they've dropped from 2000 people to 1020. But we've dropped effective capacity from 2000 to 600. So for those 1020 people they went from a 60 min wait to 102 min. Some people in standby will get frustrated by that (and why some people hate FP so much) and bail, and some people holding FP won't return and so standby can move a little faster, so the actual equilibrium wait time might only be 80 min.
Now, those 420 new riders came from "somewhere," so you think that might mean there's a smaller line wherever "somewhere" was. But we've also freed 980 people from standby (plus the people that got frustrated and bailed) and they can now go "somewhere" too. And not only can they replace those 420 people, there's enough people to double that, with some more left over. So wait times at "somewhere" can go up too.
And here's the thing, this is true for FP+ but it was also true for legacy FP. What most likely has changed is the number of "new" riders. Legacy required you to wake up on time, get to a park, etc. So maybe the net effect was there were only 5-15% of "new" riders, so wait times went up less, and it affected fewer attractions. FP+ allows for a much larger volume of "new" riders and so the wait times can be more drastically affected, and it's on every attraction people would view as "worth doing." Basically, all FP has a negative effect on wait times for the standby line, and that's not something legacy FP lovers want to hear, because if shorter wait times is the goal, it should be gone entirely (just increase capacity instead).
Now, from Disney's perspective they went from "420 unhappy, non-riders walking around and 980 stuck in a line," to "1400 happy riders walking around." Which group do you think spends more money? Makes it easy not to care about the 1020 unhappy people still stuck in the standby line only now for 33% longer. And they didn't have to mess around building expensive new capacity in each park.