Another reason not to consider Aqua is that it is designed for city use. Using it on long route won't be much beneficial. It won't give you good economy (Though still better than what City would give you) and there would be lesser cabin space. I wouldn't suggest an Aqua for your usage.
As for Prius, do note that there are very less competent people who know how to diagnose and fix the car (same goes for Aqua). If you get an unfortunate event on the route while you are in some rural area, especially on the patch between Sukkur and Hyderabad, you would be stuck big time and the probability of anyone having the skills to help you will be very less. I, living in Lahore, can't find many competent guys who can work on my Aqua, so I doubt you would find someone if something unfortunate happens in no man's land. Personally, I had to learn all the stuff myself to solve a simple problem in my Aqua.
Apart from this issue, the Prius is a really good car, both for highway and city use. It is comfortable, has a lot of features, and returns really good fuel economy.
The choice is yours, though.
