NiMH pros - works in lower temps, longer experience with technology LiIon pros - lower weight LiIon cons - less thermally stable when charging, catches fire when not well managed.
Yes, effectively, you take what you get - but in reality, there is almost no advantages either way - but, yes, certainly differences. If you're in Australia or Middle East - you take a NiMH because that's all they offer. In Asia, particularly Japan, only Li-ION was offered. Get a PRIUS v - you can only get a Li-ION. There have been so many threads on this topic - the OP should do a search. Might be easier to do it via GOOGLE search, but mention "PRIUSCHAT" in the query. I've got NiMH - which I'm happy with - been proven technology for much longer than Li-ION - and potentially doesn't lose capacity at the same rate as (evidenced in Nissan LEAFs/LEAVES) Li-ION.
NiMH has had a complicated legal/IP history. Things allegedly got better a year or two back with a patent expiration but cheap results haven't exactly stormed the marketplace. Lithium ion isn't free of lawsuits and arguments, but things are easier for users of this chemistry. From a certain point of view, NiMH showed up exactly at the right time to get clobbered in the courtroom by Big Oil to prevent electric cars from taking off. It didn't get used in many other places- some 1990s laptops and flashlight batteries, a few industrial installations. Meanwhile lithium ion showed up at the right time to enable so many other portable electric/electronic applications that nothing could stop it, and it was only a matter of time before it wound up in cars.
For the Prius the NiMH has a proven record and has supposedly been improved in Gen 4 For the Prius, unless you are in a cold climate, just evaluate the vehicle on its other features.