There are only two possible ways lines could be net longer due to FP+ (or legacy FP for that matter). First, guests could be experiencing a greater total number of attractions than they had previously. I think that's a good thing and would gladly take longer standby waits if it means I get to actually do more stuff. The other possibility is if rides are being sent out with empty boats/trains/vehicles at a greater rate than they had been previously. That's unlikely.
This is how I explain, why lines can be longer. Think RCT, every guest has a thought bubble with how long the are willing to wait for a specific ride. If the thought bubble number is higher than the current wait, "I will wait 75 min, the line is only 60 min," the person enters the queue. If the the thought bubble is lower than the current wait, "I will only wait 45 min, the line is 60 min," the person skips it.
When there was no Fastpass at all, and a ride with an hourly capacity of 2000, in order for the line to be an hour you needed a constant stream of 2000 people with thought bubbles of 60 min or more entering. Might be hard to do, that's a lot of people.
Enter Fastpass. Who gets one? The people who were willing to get in line when it was 60 min, or the people who skipped because the wait was too long? My theory, the people who SKIPPED the queue are more motivated because getting a FP makes the difference between riding and not riding. So when the ride switched to 80% FP, you lower the effective standby capacity to 400 people per hour, but you may have only dropped the number of actual people in the standby queue from 2000 to 1000 (the other 600 FP's going to people who previously did not enter the queue). Whatever the ratio of group A (original standby) to group B (skipped the ride) makes the difference. This is also an indication of how under capacity certain attractions are (like TSMM or Soarin) if group B was huge, group A won't get enough FPs to shrink standby as much as they shrunk effective capacity. FP+ also increases the likelihood of someone from Group B getting FP's because now they don't even have to get up, get to the park, and run around they can do it in their PJs at home.
So now we've theoretically got 1000 standby people, who still have thought bubbles with "60 min or more" but they can only move at a rate of 400 people per hour. That's a 2.5 hour line if everyone stayed. Not everyone will stay, as their thought bubble won't match up with the current wait time. You'll lose the people who max at 60-70 min (those probably were the people from the original standby who were motivated to get a FP and were part of the 1000), but retain the ones willing to wait 90, 120 or indefinitely. So the equilibrium point gets pushed out to something larger than 60 min.
The mistake I see people making is they think that if the wait maxed out at 60 min pre-FP, that the wait time won't grow past 60 min with FP. But that ignores that the effective standby load rate has changed (even if total capacity remains the same), and so it takes fewer people in standby to maintain a certain wait, and it also ignores that many people pre-FP might have had thought bubbles larger than 60 min in the first place. Those higher waits just didn't come into play because there weren't enough people like them. Or they think that all the people holding FP were in the pre-FP standby queue and not from group B. FP would work fabulously, if not for the size of group B.
Now, those people who weren't riding that now are, could mean a line is shorter somewhere else (they are now at a different place in the park) but "wait time adverse people" are that way for a reason and could just as easily have been at the hotel pool, taking a nap, or some other activity other than being in a ride queue or they were doing an attraction that already didn't have a line (HoP, Stitch, Tiki Room, etc) and so there may not actually be a shorter line anywhere.
Essentially, wait times are up because there were always lots of people who skipped rides, that now have FP, leaving the people willing to wait the longest (least motivated to bother with FP) still in standby queues and in greater numbers than the effective standby load rate. (it's easier to find 400 people an hour to wait 60 min than 2000). Secondly, when people feel like they "missed out on FP" they may adjust their thought bubble "because they feel they have no other choice." So in a pre-FP world where people thought "I can still ride this by coming back later, or getting up earlier tomorrow" so my thought bubble is "45 min." May now think, "there is no good time to ride anymore, if I want to ride, I need to be willing to wait 90 min." More people with bigger thought bubble numbers = longer waits.