In the first Defense Grid game, Missile Towers had an important, unique role: they were the most effective thing for shooting down flying aliens. But there are no flying aliens in Defense Grid 2, so Missile Towers have been reworked to... essentially the same thing as Meteor Towers, as far as I can tell.
They're slightly more expensive, but not by much, they have the same extreme range, lower damage but they more than make up for it with a much higher rate of fire and a far better projectile velocity. It makes me wonder, is there any good reason to prefer Meteor Towers over Missile Towers?