Good question. I have several different bikes I ride and I've noticed the same thing. I think part of it is geometry, and changing the handlebars and/or seat position may help that. But you can only do so much with those kind of adjustments. Seat tube and head tube angles, fork rake, and overall wheelbase are what they are and you have to just adjust to them.

Most of my bikes are pretty upgright. When I got an old Schwinn Prelude with downtube shifters recently, I had a bear of a time trying to get comfortable on that thing. My solution is to keep the physical adjustments to a minimum and just try to get used to each bike for what it is.