Atm there is no choice really what engine to take. Of course I can decide to research better engines, but then when I design a new ship I will basically always take the best engine, so no real choice there.
It would be cool to have an engine tech, or a version of each engine, that moves a random number of tiles each turn. It's average would be the same as the engine it is based on (e.g. 5) but the ship would actually move a number between 1 and 9 each turn.
The story for that tech could be that every engine can be modify to ride currents in subspace while folding space, or something like that. The AI wouldn't have to be modified for that tech, because the *average* speed would 5 in the example, still I could feel lucky and use them for ships I really need to go somewhere fast - hoping that luck holds and I get there fast. I could be unlucky of course and only move 1 or 2 tiles for a couple of turns.
Still it would be an element of insecurity the player can choose to ignore, or could use to take a chance. I cant think of any pathing / whatever problems for the AI, for its internal computations it could just use the average speed that engine would compute.
It could also be a tech that allows the player to choose a "subspace surfing" version of every engine at ship design.