You're probably right. I suspect that the current Plug-in Prius was mostly a trial run for the prius using an admittedly small lithium battery. Now that Toyota's engineers have some real world data from owners on how reliable lithium batteries will work in the prius, they're probably looking at the feasibility of a larger lithium battery in the next gen PiP. I just hope the Toyota leadership doesn't completely cripple the PiP in favor of advancing the FCV at all costs, or they're going to lose even more sales to competitors. I'll admit I was a bit leery of multiple battery types and/or sizes in one car at first, but it seems that other carmakers are looking at that option as well, such as the next gen Volt and Leaf. I'm guessing it's mostly a cost-cutting move until battery prices come down more with a larger economy of scale down the road. But if they play their cards right, this may help make EV's and plug-in hybrids more viable in the short term, and more acceptable to the general public in the long term.
