Don't forget aerodynamics. Shuttle suffered from all sorts of buffeting that a smooth cylindrical rocket would not. The complex shape also meant more unpredictable asymmetric vibrations. A liquid-fueled shuttle would still have been a rough ride.
And shuttle took a much more aggressive path. SpaceX rockets aim very high for longer burn times (more up, less sideways on first stage). It is technically a less efficient approach but allows for the recovery trickery.
According to the briefing video above, smoother than the Shuttle off the pad (for Falcon), which is the lower-atmosphere phase with more aerodynamic interactions, rougher following Falcon MECO, under the single-engine second stage. During the equivalent flight phase the Shuttle has shed its solid rocket boosters and consists of the three space-shuttle main engines (SSME), and the external tank. Still not a vertical stack (so subject to greater structural dynamics), though the thought occurs that three engines might be smoother than one.
There can be other effects as well --- the Saturn V had significant issues with "pogo oscillations", which are just what they sound like: strong periodic variations in vertical acceleration. Falcon 2nd stage issues might be similar.
And shuttle took a much more aggressive path. SpaceX rockets aim very high for longer burn times (more up, less sideways on first stage). It is technically a less efficient approach but allows for the recovery trickery.