I own a 2002 Dyna Super Glide Sport and have ridden many Softails, mostly Heritage Classics.
I'd say the Softails have a slight edge over my model Dyna. This may simply be because my Dyna has the narrow front end and tire and all the Softails I've ridden had the wide front end and tire. My Dyna seems more sensitive to inconsistencies in the pavement but also handles more responsively due to the narrow front tire.
My Dyna has pegs vs. the footboards that come on Softails. Footboards are really comfy on longer rides though you do lose some lean angle.
Suspension-wise, I'd say they both have about the same level of "comfort". Though my model Dyna has fully adjustable suspension front and rear.
Also, my Dyna has the unbalanced rubber mount engine vs. the Softail's balanced rigid mount engine. So there's a different feel to them due to that as well.
So again, I think overall the Softail has a slight edge over the Dyna for comfort on long freeway or highway rides.