At a quick glance:
Mk. I: Good firepower, good cargo capacity, good armor...only weakness is that it is slow. An interceptor that gets behind it and can threshold that armor can tear that engine out in very short order.
Mk. II: Ye dice, but that's a gunship! If real fighters are unavailable, I'd use this as an escort gunship. Also useful as a specops or high-value-cargo transport. The low speed is still a weakness to be exploited, though.
Mk. III: Dedicated infantry transport. Boosted armor(except the tail :() and the two platoons of troops means this would also work as a long-range specops transport, though I think I'd prefer to use it as a customs shuttle or boarding pod against very slow targets.
Each one does beat out the Mk. VII in certain areas(especially firepower and armor), though it still has its advantages. The greater thrust makes it better able to deal with fighters and to take engine crits and still live, and the range is phenomenal. It's a difference in attitude, to me. The Mks I through III are very expressly built to operate in combat zones and deliver their cargoes while under fire. The Mk. VII is more of a utility shuttle that won't automatically die if it stumbles into a combat zone.
