If you don't mind being a little "Freddish" and adding a little weight to your rig, a Thudbuster and / or a Brooks spring saddle will smooth things out.

Sometimes you have to get your butt off the saddle, that's just the way it is, and either bunny hop, or at least semi-unweight front then back.

For really trashy conditions, you cannot beat an MTB, it's designed for that. It's slower, but if you want a great CV and leg-muscle workout, you can achieve it by pushing yourself hard. You can put on 1.5 inch slicks and go pretty fast, actually. You take on potholes, cracks, and pavement buckles with impunity, and have no worries about flats, damaging your bike or yourself.

For somebody wanting the smoothest ride on crappy surfaces for a roadbike, Specialized Roubaix is possibly best, with its fork and seat-stay Zertz elastomer inserts. If riding on 23=25 mm tires.

On the other hand a Cervelo RS, which I have, can take 28 mm tires, which are more cushioning, especially because you can run lower pressures, and hardy. But if I just want to ride and not care about road surface anomalies, I love my Specialized Stumpy with Armadillo tires. Potholes, tire wires, glass, goatheads, it just fends them off with aplomb. It takes something like a nail hit at the wrong angle to get a flat. I get as great a workout as I put into it. I can keep my HR at under 130, which I like for long rides, or run it up to 150-180.