No, just the opposite... I get less soreness. The more biologically-adept may be able to give a better explanation, but changing speeds seems to change up muscle activation patterns, which reduces fatigue. Terrain also plays a role, though. Almost all of my long runs over the last year or so have been on trails, most in mountains. Keeping a steady pace is impossible, and I really like busting out the occasional sprint.Oddly, I don't notice a significant difference in the point of glycogen depletion. I reliably hit a wall around 13-16 miles regardless of pace or consistency if I'm not consuming calories.
As far as the actual training aspect, I don't know that I have enough data. I'm faster than I was back in my "constant speed long run" days, but there's a lot of other variables that could affect it.