Whilst I can empathise with your problem, I am afraid that I cannot be much help. I am convinced that you and only you can decide what is important to you, and with two such differing cars it's a bit like trying to compare a pet rabbit with a pet dog, both are excellent in their own way, but at the end of the day they are completely different animals.
I chose my RX because I wanted the size, comfort and "waftability", but I can see that a Prius would give reliability at a lower cost, and if cost is an important factor then that could sway the decision. The problem is of course, if you follow that line of thought to it's logical conclusion you would end up with a Smart Car.
Best of luck, but remember that in the end you only have to justify your decision to you.