Here is my idea:

Several missions produce unique, desirable artifacts that only allow a limited number of uses.

How about an artifact, purchasable ONLY with galaxy points, to assure income to the game, that allows you to choose any mission that you have already finished, and reset it back to Zero, to allow you to do the mission again, and gain the related rewards.

"Temporal visitation licence", maybe? allowing the player to travel back in time and re-visit the adventures of a particular mission.

Certain missions are simply to powerful in terms of rewards. Can you see how it would be game breaking to have people with unlimited Galviz Devices (race change) Trellith Structural Energizers (structure +50%), etc?

If it cost 60+ GP it wouldn't be OP for the Glaviz mission, but if this was done, there are a number of missions (such as many of the Trellith) that would need to be excluded to keep it from being OP.

The mission that gives you your mission invincible planets would need to be excluded as well. Though so many people would probably buy the needed arties that it would give Dan a nice incentive to leave those included so he could make some good money off that. Can you imagine having 6 invincible Rift planets?

The problem lies in the Missions people would WANT to repeat are the missions that we really can't allow a limitless repeat (unless say you go and make it limited to one extra mission ever or something)

While the price of this artifact might be fixed, the amount of the artifact required to reset a mission could vary. For the less impressive missions, it could just require 1. But for more powerful mission that rewards CCM, energizer, ergo etc it could take more, up to maybe 5 for the first reset. Only missions that reward items that is completely unable to trade, such as the project planets needs to be excluded. All other thing can be traded(thou could be complicated and no longer possible onto certain planets) and might as well line Dan's pocket than them merchants.
Also, each time a mission is reset, the next reset should become more expensive. This can either be linear( the nth reset cost n times as much) or exponential(price double every time) can be discussed but there needs to be an increase.