Unfortunately, the longer lines won't just be for attractions with "overlapping" Fastpass systems. Once FP+ is fully rolled out, there will be FP+ lines slowing down the queues at every single attraction that didn't offer traditional paper FP but which will have FP+. (E.g., Carousel of Progress, iasw, POTC). This means that even the old reliable "walk-ons" aren't going to be walk-ons anymore. FP+ lowers your wait for exactly 3 attractions per day -- the 3 for which you can use FP+ -- and increases your wait for everything else.
It's this line of thinking that makes me think that some people aren't seeing the big picture. (And I'll admit it's a very complicated and multi-faceted picture to try and comprehend)
To get one correction out of the way, CoP does *not* have FP+. Everyone keeps snarkily saying it does or will, but it doesn't. The only time CoP has ever had FastPass was when some nearby attractions would spit out a "Bonus FastPass" to try and get crowds to notice these large-capacity attractions.
Now, on to my reasoning on why I don't think FP+ will be the horror story of mega-long lines that everyone else keeps making it out to be. (I start with the caveat that these views are for *after* the full rollout and everyone can use FP+ and regular FP is gone, not the weird hybrid dual system that's in place now).
First, imagine a park (we'll say MK) with *no* FastPass system in place at all. This is pretty much how MK ran before FastPass in 1998. There were just queues for everything. People wanted to ride a ride, they waited in line. Walkways were relatively free and open because a large chunk of people were standing in a queue.
Now, imagine that same setup, but *everyone* walking into the front gate was given a single Front-of-the-Line pass. They can use it to jump the queue on *any* ride they wanted. Everyone gets just one, so there isn't a huge difference between only queues and queues-plus-one-pass. Most FOTL passes will be used to skip long lines like the Mountains. Some will be used for favorite attractions like Pirates.
Now, increase that to two FOTL passes when you walk in the gate, but you can't use them on the same attraction.
Now, increase that to three FOTL passes. Many will still be used at the Mountains and other E-ticket attractions, but some will get used at lesser attractions with large capacity like the Mansion. Will those used at high-capacity attractions like Mansion get in the way of a huge number of Standby guests? Probably not.
That's what FP+ will be, except the three FOTL passes will be spread throughout the day rather than allowing people to redeem them whenever they want, thereby keeping possible overload situations from happening.
This is why I don't think the FP+ system will be the catastrophe that some make it out to be. It'll also bring back less-congested walkways because there won't be as many "virtual" line-holders and people will be in queues more than walking around as they are now.
-Rob