Rather than the seemingly endless mission nerfs, I have a suggestion...
The clockworks gates already have fees for joining at t2 and t3 without having previously cleared to that point from above. With the mission system, these fees have become largely pointless - people just skip to the content they want via the mission interface.
Since it's really the extremes of farming that the nerfs aim to correct, why not charge players in CR to replay missions.
The way this would work is that each time a mission is replayed, a small fee in crowns is charged based on the mission tier and the number of times that mission has been replayed in the last 24 hours. This way, we can still help our friends in missions, and replay enjoyable missions often, but playing RJP, twins, and FSC over and over and over eventually won't be any more profitable than just playing levels through a gate.
I'd suggest 10 CR per run for tier 1, 50 CR per run in tier 2, and 100 CR per run in tier 3. With this system, I estimate it would take roughly 15-20 runs before a particular boss mission becomes less profitable than other content at the same tier, so farming's still possible, it just would have less of an impact than it does now.
The gates already have a way to bypass the T2 and T3 fees; do the tiers before where you want to join, leave for shenanigans, come back later to the same gate, free entry. To be more specific: you clear T1 on a Roarmulus gate and have cleared the warden. For whatever reason you have to leave for a while. You come back later while the same gate is still active. You open up the Clockworks menu, select to start at the beginning of T2, no entry cost because you already cleared it on that gate. Does no one else know about this?
Charging for replaying missions means punishing all mission replays.