Sounds perfectly normal to me. Yes, when towing a heavier trailer, you are going to feel every crack in the road. This is THE reason why I quit driving Interstates, especially in Indiana that has very bad expansion joints at bridges, road construction that leaves roads a mess, uneven lanes, pot holes, and everything else. Amazing, back country roads in Indiana are smoother than almost any Interstate in Indiana.
The heavier weight on your truck??? yes.... you will now discover why you see 18 wheeler truck parts laying all along the Interstate ditches.