I currently own an Aprilia RS 457 and use it for a daily 20 km one-way commute (about half open road and half bumper-to-bumper traffic). The RS 457 is uncomfortable, so I plan to sell it and buy a more city-friendly bike. I want something lightweight with a low seat height (I’m 5'6"), a refined engine, plush suspension, and the ability to cruise comfortably at 100 km/h for occasional short highway runs.

Since you are used to a good amount of performance, we'd suggest you move to something like the Triumph Speed 400. This bike will meet your needs of having a comfortable riding position as well as a reasonably low seat height. 

There are more comfortable options available, but almost all of them are adventure bikes with relatively tall seats. If you can get along with a taller seat, we'd recommend options like the Royal Enfield Himalayan 450 or KTM 390 Adventure as good replacements for your Aprilia RS 457.