Thanks for the replies. I'm a little less confused now. My bike that I don't like, I think it's more the aggressive handlebars that have way more drop than I'm used to and are narrower than I'm used to. My LBS tried to set it up as close to the Trek as he could, but it's a different geometry frame that's less upright.
Plus the gearing is too strong for me.

I test rode a Cannondale that I liked. It was 56 and felt fine right off the rack. All they did was set the saddle height for me, and it was very comfortable, like my Trek. Guess the numbers don't necessarily mean as much as I thought.