Just a mathematical breakdown really. Let me state some numbers that are genrally accepted to be true based on info that is out there. MK averages ~60,000 guests per day. According to Touring Plans, 70-80% of a queues capacity is alloted to FP+ (let's split the difference and say 75%). Now let's look at a popular ride's throughput. I'll use Splash Mountain for one example (it has a faily high hourly capacity) and Peter Pan's Flight for another example (faily low hourly capacity). Splash has a throughput of Approx. 1800/hour. Peter Pan's Flight has approx. 1100/hour.
So on an average 14 hour park day, Splash moutain will accomodate 25,200 guests. If ~75% of those riders are pre-booked FP+ riders, that's 18,900 riders. This means that 68.5% of that day's guests, if they want to try and ride, are subject to a very long wait, longer than if there was no FP+ to begin with. Peter Pan is worse. Do the same calcs and 80% of that day's guests, if they want to try and ride, are subject to a long wait, longer than if there was no FP+ to begin with.
By charging for it the % of people that has a FP+ should be drastically lower than the ~75% of a queue that is taken up by it now. Depending how they price it, I'm guessing the amount of the queue that is FP+ will probably be maybe 10-15% Opening up much more of the line to standby and reducing the wait for standby, improving the experience for a much larger number of people. And if genie works as they think it will (by guiding the majority of guests in an overall optimal dispersion through the entire park) then that standby wait in theory could get even better (but that's the biggest unknown that I'm curious to see how this aspect that Disney hopes for will pan out).
There was never a guarantee of the availability of FP+ to everyone who wants it. And by that I mean sure, everyone has "access" to FP+, but the large majority of a given day's park visitors do not in practicality have access to the best FP+'s.
Oh! I love the math
I keep speculating that the new 'wishes' will be free for certain levels of resort guests. Your numbers makes me think more about how that might be distributed.
It made me go and do some totals for the different levels of Resort guests - assuming full capacity at the resorts and an average of 4 guests per room, those numbers could break out:
Value Resort Guests: 44,432 - (1/4 11,108)
Moderate Resort Guests: 29,540 - (1/4 7385)
Deluxe Resort & Villas Guests: 52,984 (Includes all the resorts eligible for EEH) - (1/4 13,246)
Good Neighbor Resort Guests: 18,964 (estimate on a couple hotels, includes non-disney resorts in the Early Morning Hours) (1/4 7385)
If 1/4 of those go into a park a day, that accounts for 36,480 guests.
I still think Disney is going to give some free FP+s to resort guests, I think the outrage will be too much.
I think then they could still offer '3 wishes' to Value guests, 4 wishes to Moderate and Good Neighbor and 5 to Deluxe.
Charge for Fastpasses or Wishes to out of resort guests to recoop the loss of resort income.
But maybe it takes 2 wishes to get a Fastpass to the Tier One of FP from the old system?
MK rides are all in the same FP Tier. So everyone would have 3 minimum.
Epcot Tier One rides are: Soarin', Test Track, Frozen and Fireworks seating. (assume Remmy will be here)
Hollywood Studios Tier One rides are: Slinky Dog Dash, Millennium Falcon, Mickey & Minnie's Runaway Railway
Animal Kingdom Tier One rides are: Flight of Passage, Na'vi River Journey (really think should be Tier 2)