I agree that from an in-universe perspective, the newer ships should and would outpace the old.
Very true - although not necessarily in the real world. Destroyers got a lot slower after WWII, for example, as there was no point in them maintaining 35kt+ speeds any more, and endurance was preferable to dash speed. Many fighter aircraft ceased to be multiply supersonic as well. And then there are the supersonic passenger transports... Basing travel time calculations on known 1940s-50s speeds and as such realistic predictions and extrapolations would result in completely erroneous figures in these cases.
In the Trek universe, though, speed would appear to be of value despite the twists and turns of history.
Still, it's not that outlandish to think that Picard's juggernaut would be sluggish in comparison with Kirk's nimbler ship. Or that there has been minimal evolution in warp propulsion between TOS and TNG. After all, there appears to be a "galactic norm" to how fast ships are going (or else we could never have chase scenes!) - which means average starfaring cultures are going to plateau on their warp speed evolution and then get stuck on that plateau for millennia, allowing for the observed synching.