Someone else may have suggested this before, so I cannot take credit for all the ideas in this post. When you have a mission, suppose that you were required to delve into the Clockworks to accomplish it. For example:
Suppose you are assigned "Skies Under Cradle," which is an Aurora Isles mission. Kora will tell you which gate and depth it is located in, and the player is to go there. But here's the catch: it may not be in rotation yet, as per normal Clockworks functionality. So you may have to wait sometimes. This will make the players experience the Clockworks the way it was meant to be.
I had an idea about the supply delivery missions, too: taking cues from the Winterfest event, when you purchase a supply pack and start the mission, the pack is placed on your back, and you must travel through the Clockworks to deliver it. The catch is that these packs slow you down. Compact, Standard, and Deluxe supply packs slow you by -1, -2, and -3 MSD each, respectively, and some missions will require you to carry up to two packs at a time.
Opinions?
"Kora will tell you which gate and depth it is located in, and the player is to go there"
Missions have a fixed depth, to make the difficulty linear. And for that you'd also need players to deposit the right minerals on the right strats. It could take a lot of time to get what you need.