I think that if you're looking at having a mission-based tournament, you can go about it in two basic ways.
You can have complex, fun missions, but probably sacrifice balance. Or you can use micro-missions or scenarios that have a good chance of being reasonably balanced, but may not be as inherently interesting. Environmental changes, such as substituting derelict freighters for the asteroids, would work very well I think.
In a tournament I would err on the side of balance.
And of course, skirmish will always be king for tournaments, especially big ones. But mission-based tournaments could be feasible and fun, so I think they're worth some attention.
Some scenarios I'm floating for use in 'tournament setting':
Edited by Babaganoosh