There isn't much they can do if the story requires both that a chase from planet A to nearby planet B take an exciting three hours, and a Klingon ship arrive from the Empire to meet our heroes at the destination within no more than six hours lest things become boring. Sometimes warp simply has to be both X and a thousand times X: consistency is ruled out as an option from the get-go.
Doesn't mean there couldn't be excuses, of course. Quite possibly warp gets faster if you spend more time at it - or alternately you can risk much higher speeds if you know you will only be doing them for three hours rather than three months. But the idea that warp factor X would give a significantly higher speed along a specific "space lane" is to be treated with utmost caution, because if the speed advantage offered by an "express lane" truly is significant, then this should be reflected in dialogue big time. No more dabbling in "warp factors" - the valiant skipper should be solely concerned with the question "Where is the nearest express lane?".
Yeah I agree with avoiding the "express lane" factor. That just complicates things.
As far as long Starship chase scenes, good editing / cutting can make it interesting.