All my road bikes are set up as similarly as possible, considering they range from a 1980s steel frame to early 1990s carbon fiber to 2012 or so carbon fiber. It's fairly easy to set up the first two comparably because both are traditional diamond frames. The 2012 bike has a compact frame with sloping top tube and took more fiddling to set up to suit myself.
The main differences I notice have little to do with the frames but more to do with wheels, tubes and tires, and gearing.
The old Suntour GPX rear derailleur on my Ironman always felt draggy until I replaced the sintered bearing jockey and pulley wheels with sealed bearing wheels (same or similar composite material, something like nylon I think -- Bullseye aluminum wheels are similarly smooth but a bit noisier). That fixed the draggy feeling -- sintered bearings, dry or lubed, just can't compare with sealed ball bearings. So now all my road bikes have some version of sealed bearing jockey and pulley wheels.
Crank length might make some difference. With age and arthritis I notice more slight hitches in my pedaling, depending on how stiff I am on any given day. Maybe some minor differences in shoes, cleats and pedals too -- I have Look Delta on the older bike, Shimano SPD-SL on the others. Very similar floating cleats but not identical.
Another difference I can feel and measure to some extent is the diameter of the chainring and rear cog in my preferred gearing for a given route -- mostly roller terrain in my area, no serious climbs but no extended flat and level terrain either. It feels more efficient when I'm in the big ring and middle cog -- which pretty much meshes with the current conventional wisdom in the pros that larger diameter chainrings, cogs and jockey/pulley wheels are slightly more efficient, enough to offset the slightly heavier components.
And I've noticed that using any rear cog smaller than 13 teeth feels like grinding coffee. The 11 and 12 tooth cogs in my newer bike never feels smooth. It's just a mismatch between the chain design and cogs (I forget the term best used to describe this but there are techy articles discussing this). The standard bicycle chain link length seems to lose efficiency quickly with cogs smaller than 13T.
Overall I'd say my smoothest feeling road bike is my 1989 Centurion Ironman with the current 50/38 chainrings and 13-25 or whatever freewheel. Mostly because the 50T chainring happens to work best with the three middle cogs in the freewheel on my usual 20-35 mile route, so there's little deflection of the chain, no sharp bends around small cogs. And maybe the 172.5 cranks suit me a bit better than the 175 cranks on my 2012 carbon fiber bike. I also liked the 170 cranks on my 1993 carbon fiber Trek 5900 -- not a huge difference, but pedaling felt smoother than with the 175 cranks.
It's all very subjective and none of my bikes shows any significant advantage over hundreds of rides on the same familiar routes. Some of my fastest Strava times and PRs were on the Ironman back in 2017 when I was probably in my peak conditioning (for an old dude). I've beaten the Ironman times on a few roller coaster segments with the carbon fiber bikes, so maybe there was a small edge to the lighter overall weight.
But there are so many variables it's tough to pin down to any single factor -- frame design and composition, wheels, tires, tubes, gearing, drivetrain, etc.
I will say that as my neck pain worsens (arthritis and cervical spine stenosis and spondylosis) I'm preferring the 2012 Diamondback mostly because I have it set up with the least drop between saddle and handlebars, maybe an inch drop. My Ironman has closer to 1.5" or 2" drop even with the stem fully elevated to the limit line, and the top tube is slightly longer so I'm more stretched out. And the early '90s Trek 5900 is set up much more aggressively so it's a real chore to ride now with a bum neck. Bike fit plays a big part in overall ergonomics and how a bike "feels" to pedal, especially with an aging body that's beat up from injuries and the usual aging stuff.
I'll probably replace the current 120mm horizontal stem on the Ironman with either a 90mm stem I have in a box, or an angled riser stem, and possibly a newer compact drop bar with less reach and drop. That might bump the Ironman back into my favorite spot. It was always pretty comfy on rougher roads as the frame is slightly more compliant than my road racing oriented carbon fiber bikes.