My guy's conformation is a bit straight. When he came to me he couldn't hardly trot in a straight line with a rider and his trot actually resulted in me pulling groin muscles more than once just trying to stay on. It was horrible. With a million and one transitions and teaching to carry a rider and himself, it's now passable. I doubt it will ever be fanstastic, but it's a million times better. We're even working on a 'jog' now, something I could only dream of a year ago.
Relax, work on yourself on other horses with better trots, work on him, but I might also consider just posting and giving both of you a break too. Some horses just don't have an easy trot.