Hopefully if this new system works correctly, the wait time for the regular lines will drop. If you're controlling how many guests enter the FastPass line, that's less that you have to halt the standby line for. Less FastPass guests means more regular guests get to enter onto the attraction.
Let's say an attraction gives out 2,000 FastPasses. If they come back all spread throughout the day, it's a pretty good flow between the 2 lines. However, if they all come back at 5pm at night (which they could with the current way it works), the FastPass line is now not very fast, so the regular line has to come to a complete stand still, while only FastPass is being let onto the attraction.
Hopefully it'll work. The only thing they need to do is let guests know before they get their FastPasses. Signage is needed, as well as Cast Members reminding guests. Information on the websites and maps would help as well.