I think it is important to keep a few things in mind here.
First off, the ride line management aspect of this system is a massive undertaking. While Disney does have tons of data to work from, you never know how a big change like this is going to pan out until you actually implement it. For that reason, I think they have been very wise in bringing this system up slowly, with significant limits at first so that they could gauge how it was working. I don't think this is going to be the last change to the system. I believe they will continue to watch how it is working, and make further changes down the road.
Secondly, ride line management is just one aspect of the My Disney Experience system. Ultimately, the ability of the system to personalize guests interactions with cast members, and interactive elements of rides / queue lines / etc. may well be the biggest plus of the system.
I still think it is early in the day to call the system money poorly spent. I think there is a lot more to this system that we haven't seen yet.