I had a 2004 and currently have a 2009 Prius standard; we got Thule racks that have rubber adapters that fit into the "rail" on top of the car, and clips that grip underneath the roof line between the door and the roof. It is a solid set up. We have two sets of Thule j-racks that cradle the kayak, and the roofline seems to be short enough that my 5'1" wife can load and unlead the boats.
I believe Yakima also has a system that fits the car.
A roller system that loads from the rear could be tough since the back of the car is a good distance from the rear rack bar. If you need a load-assist attachment for the racks, go for something that loads from the side.
Length is no issue if you tie down the front and back...and the Prius has good tie down points beneath both the front and rear bumpers on each side. I've carried an 18' long canoe at highway speeds with zero issues, although a good cross-wind with that load on that car could create some white-knuckle moments.
Touring Kayak Paddles
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