Well, looking at 3% to 5% is one prospective; another one would be to compare the relative fuel efficiency loss due to AWD. For the Prius, it's twice as high as the for Sienna. But the real surprise here is that in the Prius this higher loss occurs despite the fact that the rear motor is much smaller .... in fact, one might even question its utility.
From what I understand, Toyota is very fond of the Ni-MH batteries because they are more resilient, present a lower fire risk, tolerate low temperatures better, and probably have lower manufacturing costs than comparable Li-ion batteries. I may have mentioned earlier that Toyota now has a "bipolar" Ni-MH battery as well, with much higher (2x I think) energy density than the "regular" Ni-MH. I do not know if this battery will make it to the North American market, though.
Do you mean globally, as in for example Li-Ion in Europe and Ni-MH in the Americas?