I have some pretty fast transport ships I create and I can envision other players getting even more extreme.
It's actually a separate issue but related. The "I can go around you" is an inherent problem in all TBS games. You can make your moves and the other guy must sit still. The bigger the movement range per turn the worse this problem gets. Transports stuffed with engines take this to the extreme as capturing planets is a powerful ability.
In an RTS game the problem goes away because even a slower ship can intercept a fast one and initiate combat if it's positioned right. We, of course, don't want an RTS game so the solution needs to be something else.
The usual way is to introduce an intercept rule that either blocks your move into an area controlled by an enemy unit, or making the move initiates a combat. Civ is an example of the former but I think the latter would fit better to the GC concept. In Civ you are moving forces on a battlefield so they are flanking and counter-flanking each other so a blocking ZOC rule makes sense. In GC it's space ships flyiing around so it's about trajectories and interceptions and so a "can force combat" rule makes more sense.
Try to move a fleet into the range of an enemy fleet and you get the choice of aborting the move or having to fight it. This would cure the fast-transport-exploit as you'd have to clear the target area from enemy combat ships before your transports could invade. Would make more sense than your transports being able to just fly past the enemy while they conveniently sit still and do nothing...