Yeah, what Captin...er...Poo said. Missions are almost like instance hordes and bosses, but less predictable. That's good isn't it? We'd just need to add very high level missions with uber bosses and really great stuff.
But not codies.... I'm uncomfortable with the notion of item farming. (OTOH it annoys me that every single wreck is always bloody looted.)
ps. Example, we could have a destroy-base mission. It is defended by elite fighters & caps, and mounted with pwnz0r guns. But when it's destroyed lots of goodies come falling out.