First, I agree that it makes sense to focus these discussions on MK. Because of the lower number of rides at the other parks, it shouldn't be difficult for anyone to do each of them that he/she wants to do with an efficient plan and effective use of FPs. So, at those parks, much of the dissatisfaction people have with FP+ relates to being able to do some of the major attractions multiple times, and I think that's a different discussion than longer standby lines.
Thank you for providing the dates of your recent trips. If you look at the observed crowd levels for those dates on Touring Plans, they might explain that at least part (if not most) of the reason you saw longer standby lines at the MK on your trip in 2014 is that those days had generally larger crowds than your trips in 2012 and 2013.
Here are the Touring Plans actual crowd levels for the resort and the MK for those dates:
3/31/14 6/7
4/1/14 5/7
4/2/14 5/6
4/3/14 5/7
4/4/14 4/6
4/20/13 6/6
4/21/13 4/4
4/22/13 3/2
4/23/13 3/5
4/24/13 2/2
4/25/13 3/5
4/26/13 4/5
4/27/13 6/5
4/17/12 1/5
4/18/12 2/3
4/19/12 3/3
4/20/12 5/5
4/21/12 5/4
4/22/12 4/4
4/23/12 1/5
4/24/12 5/5
Of course, I don't know if the crowd levels on any of these days were affected by weather. But, regardless, the crowd levels at the MK for every day of your 2014 trip were at 6 and 7 and the MK crowd levels for every day but one of your 2012 and 2013 trips were 5 or less, with some 2's and 3's thrown in.
Both Touring Plans and easywdw have said that, because of overall increasing crowd levels, crowd level numbers do not compare directly from one year to the next. For example, a crowd level 5 (average) in 2015 will translate to more people than a crowd level 5 a few years ago. I recall Josh at easywdw saying something to the effect that a crowd level 2 day in 2014 would be about the same as a crowd level 5 day 4 or 5 years ago. Therefore, you would have to expect that a crowd level 6 or 7 day in 2014 will have had a noticeably larger crowd than a level 3 or 4 day in 2012.
For another comparison, I looked at Touring Plans' average wait times for the 3 MK rides you mentioned, IASW, POC, and HM. For the one crowd level 6 day from your two trips (4/20/13) the average wait times were 20, 22, and 28 minutes. For the two crowd level 6 days from your trip in 2014, the average wait times for 4/2 were 21, 26, and 28 minutes and for 4/4 were 16, 26, and 29 minutes. The average waits on the crowd 7 days were higher; the highest was 3/31/14 at 27, 33, and 38. If you visited on one of the crowd level 2 days in 2013 you would have seen much shorter lines at these rides. On 4/24/13, one of the crowd level 2 days, the average wait times were 7, 8, and 13 minutes.
Touring Plans does not report actual observed wait time data as far back as 2012 so I can't compare those. But, I think the most significant thing in all of this is that the average waits for days of your 2013 trip (before FP+) are pretty much the same as the days of your 2014 trip with the same crowd level.
To be clear, I am not saying that FP+ has not had any impact on any standby lines. It is also very possible that standby lines have increased between 2014 and 2015. And I don't know if comparing other dates with similar crowd levels would produce the same results. But, at least in the case of your recent trips, I would conclude that the longer wait times you observed in 2014 were caused mostly by larger overall crowds during those visits. If you had been fortunate enough to visit on dates with crowd levels in the 2-5 range, you probably would have seen crowds similar to what you saw in 2013.