We just returned from 6 days in the parks. We utilized FP+ to its fullest potential, and used the app and website to make changes to at least half of our Fastpasses. It was our goal to interact with the system as much as possible.
While there are definitely some downsides to the system, they are primarily subjective and are only seen as downsides to those of us who knew how to use the legacy system to its fullest potential. Gone are the days of getting multiple ToT FPs in a day, or using FP in more than one park on the same day (although I strongly believe we'll see these benefits added once the bugs are worked out).
But on the flip side, this was the first time we've ridden TSMM in several years. We're not early risers, and don't "rope drop", so we've never been able to get a TSMM FP by the time we've gotten to the Studios at 11am or so (or, the Return Time was very late in the day - well beyond when we'd still be in the park). This time, we rode TSMM as soon as we arrived, late morning, because we were able to reserve the time in advance.
Same thing for Peter Pan in the Magic Kingdom. We haven't ridden it in the past several trips simply because the line is always very long, and because we've never wanted to "waste" a FP on something other than an E-Ticket (since you could only hold 1 FP at a time previously). With the ability to have 3 FPs at the same time, and by visiting the MK more than once during our trip (which will be the case for 90% of multi-day guests), we felt as though it wasn't a "waste" to reserve a ride on Peter Pan.
Another HUGE advantage of the new system is the ability to change your plans at a moment's notice. For instance, it rained on Thursday from sunrise until early afternoon. We had planned to visit the MK and use three FPs that morning. When we realized Wednesday night that Thursday morning would be a wash-out and that we'd rather sleep in and go later, we hopped on the app and moved all three of our FPs to Thursday night - without a single problem.
We did the same thing Friday morning, when we realized Disney's (lack of) transportation was putting us VERY behind in our pre-departure plans. We had 3 FPs for MK, and since it took almost 2 hours to get from Epcot to MK, we scooted some of those FPs to a bit later, and even changed the experience for a couple (since all 3 weren't available at new times with an hour's notice).
All-in-all, the benefits I've outlined above more than offset the losses we personally feel we experienced by not having multiple or park-hopping FPs any more. And I can say that because I am confident that those perks will be added back into the system eventually. Once perfected, the system has infinite flexibility.
Also, the comments about it taking several seconds to process a Magic Band at the FP scanners - false. It may have been true when they were still REALLY testing the system, but never once did my wife or I have to hold our MB against the FP scanners for more than a second or two. And it was only ever 2 if we didn't have our band facing the right way and had to shift it. The only thing that takes a while for MBs to read is at the "turnstiles". It takes several seconds for the scanners to read the bands and fingerprints - and I really hope they work on that. It takes an unacceptably long time, which creates long waits at the park entrances.