...by all rights newer ships ought to be more obviously faster (not just a decimal point faster)...
But is this true? I can think of two arguments to the contrary.
One, warships in the real world haven't gotten any faster after WWII. The technology was not perfected back then, by any means, but modern ships with better engines are not faster. They are merely more fuel-economic, have greater reliability, better acceleration, greater range. There is no good use for speed past 30 knots in modern naval warfare, because a ship can't outrun her main opponents (aircraft, missiles and spysats) anyway, and there are many drawbacks to abandoning the classic boat hullform which limits speeds to 30 knots.
Two, there is no need to assume that technology has developed in leaps and bounds across the Trek eras. Many of the starfaring species that formed the Federation after ENT had already been starfaring for centuries. They had already maxed out on their tech; if it were possible for them to build faster ships, they already would have. It may well be impossible to improve significantly on TOS or even ENT warp propulsion. One may have to invent something else, something falling under the general description of "transwarp".
Timo Saloniemi