Many observations made so far point in the same direction: speed differences make little sense and can be eliminated as a source of pointless annoyance.
- FTL propulsion can have the same pseudo-speed for every ship because it's based on the same technology: for example, a succession of "jumps" involves a maximum or fixed distance and a constant preparation time for each jump, with the only difference between ships being energy cost and device size.
- Realistic propulsion can be designed to give the same "standard" acceleration, and therefore the same travel time on any route, to any ship.
If both engines and robust materials are very good and relatively cheap, the limiting constraint for acceleration is not squashing passengers to death (rather than affording powerful engines or not breaking the ship apart) and it doesn't vary by ship type. Improved engines are going to be smaller, cheaper, more efficient, but not "faster".
If FTL speed differences (like in Star Trek) are needed, they can be simplified to a few tiers and used to forbid ships with different speeds to belong to the same fleet. Serious speed differences are going to imply different strategic movements in any case.
If limiting thrust of realistic engines according to available fuel is a normal occurrence, it can be assumed that the fleet automatically allocates available fuel to maintain the same travel time for every ship, rather than slowing down specific fuel-challenged ships. Computations are easy: fuel is proportional to ship mass.