Sore knees? Two things come to mind - bike setup and trying to push too hard a gear.
You're already (thinking about) changing out the saddle - this could/might change your riding position a bit. Realistically, I think most people can handle 20 miles on almost any bike that's setup reasonably close to what it should be for that person's body. OTOH, the further one rides, the more discomfort is likely based on incorrrect bike setup - even in terms of a few centimeters. So, I'd start there - minor adjustments looking for the optimum personalized bike setup.

Trying to push too hard a gear rather than spinning an easier gear is the other primary consideration, I would think. This remains applicable to me because spinning (high cadence/anything above 85 for me) still feels abnormal. So I have to remind myself to push an easier gear at a cadence that is not yet "normal" for me - when I do, I generally finish rides feeling "fresher".

Lastly, consider whether you're riding with your knees over the pedals or outside them. This is basic technique but has a defiinite impact on power and comfort for me.

I'm sure others have additional comments/advice. Good luck.