I had a 01 Prelude too. The seating is low in the 16 Civic but I don't think it is as low as the Prelude. It is however it is close to the ground for a family sedan. I hope that is not a negative for any potential customers who are used the trend of a higher seating position.
The (usually non-height-adjustable) passenger seat in the Civic sedan is 19.5"-20" high. IIRC the hatch was about 22", I'll have to get by the dealer and measure it again. Typical of this class car is 22".
My wife and I are used to 25" (PT Cruiser) and 27" (Soul) so this is a stretch back down.
I wish I had a longer test drive....The seats are too low and too uncomfortable, I had to adjust the driver side seat to the highest it can go so my foot could find the brake pedal ( I am 5'9" so I am considered average height) I wish the car came with adjustable pedals! The interior was what sold the car to me. But if I had a longer test drive I wouldn't of bought the car. My wife complains that her seat is too low. I bought a 2016 Ext coupe. The engine is noisy, the car rattles and it doesn't feel like a new car should feel. If I had a longer test drive I would of never bought it. This was my first Honda and probably my last unfortunately I am stuck with it for 6 years.
The problem is you didn't shop extensively enough, more than the problem is with Honda. The seats ARE low, especially given the trend to higher and higher.
Once you get some equity in the car you can go shop and try to get out of it. The plus is that car should hold value pretty well.
I've driven Forte5 SX, Elantra GT, Golf, Mazda3, and Acura ILX and overall I liked the Civic the best.
Why they do not include what I consider basic SOP equipment like a sunglasses holder in the roof is beyond my understanding.
I hope you and your wife can adjust to your car as time and miles accumulate. Try a cushion.
Driving a car you have a strong dislike for is not fun at all. Been there done that got the hat.