We are very happy with our Pure model. Believe it or not, one of the main selling points for us was that it has manual windows. My wife dislikes power windows; she complains now and then about the power locks, and it took a few tries to figure how to squeeze the rear hatch latch. Since the car is narrow, it's easy to reach across and roll down the passenger window from the driver's seat, and the windows have never moved by themselves.
The only options we ordered were a radio and power steering, which is probably unnecessary, but I remembered it took a some elbow grease to park our old VW beetle, and it has been years since we had a car without power steering. I haven't noticed any skittishness or abnormal steering at highway speed, and I think I read somewhere the steering is quicker with power steering.
We added a cargo cover from the dealer (about $150) in case we wanted to hide something in the back, and we haven't used it yet in 3 months, but the best feature is that it prevents items from falling off the cargo floor under the front seats, and it has a couple pockets which we currently use for an umbrella and an ice scraper. I also have some rubber floor mats on order to get ready for the melting dirty snow from our feet in the winter season.
We almost always drive in the auto mode, so we don't miss the shifting paddles, and the few times I have tried manual, the stick on the floor worked fine.