I replaced my wheels on my Crosstrail, since, well, rear wheel broke (several spokes and slightly warped wheel) essentially since I attempted to use it as a mountain bike with my son a few years ago. Bought new mountain bike wheels, not high quality, but stronger and it takes bumps better. I don't feel as much road imperfections like I did prior, theyre more muted. But new wheels are bit heavier and takes abuse alot more than my original wheels on trails like the C&O.
I too have two sets, one for trails, one with road tires on them. Got tired of constantly switching tires when needed.