Interaction between Spiral HQ and Haven/Clockworks
You know those missions where you have to do junk because HQ said so? Give them a hub, be it a Clockworks terminal (like HoH), a cave, even a field adjacent to Haven. You know, so we can walk there. This is more of a personal gripe about how knights tend to live off who knows where and teleport wherever they want with the magical missions menu, rather than pre-mission days when we actually walked places and the Arcade had people in it. Also, those research teams stationed in Moorcroft, Emberlight, etc.? Let us see them when we go to those places.

Mission-Clockworks integration
Similar to Spiral HQ, missions seem disconnected from Haven. Make them show up in the Clockworks as a branching path that only reconnects to the main Clockworks at the end (example: Gate Iron Potato has the following levels in floor rotation of depth 1: Mission Y entry, Construct Arena, Generic Construct level. Depth 2 will either be Mission Y 2nd floor and ONLY Mission Y 2nd floor, or it will be a rotation of (insert status) Deconstruction Zones).
Remind people about the rotations in tour missions, as well. It seems to fit better with the lore than the ready room just being off somewhere with its own perma-Vana gate. Also, it would promote collaboration between players who hire a runner (probably with an Elevator Pass) to go down to the floor they need and then invite the mission-goers when they get there and the gate is in rotation.

Enemy/loot rebalance
Make enemies harder. Wolvers/Zombies/Retrodes should be able to adjust trajectory (within reason--We're fighting wolves, not Neos), Greavers should be more fluttery, status Chromas should try to set up traps, and Gremlins should be the most intelligent, with dodging, spreading, trapping, and teamwork. Devilites should only dodge when within swing range/they notice they've been shot at, but otherwise be derpy. Since they're ranged, they wouldn't need too much advanced AI. Kats shouldn't always dash, making combos easier for both sides to complete. Bosses should also feel, well, boss-like. As in, make them able to 3-4HKO players, require intelligence to beat, and take longer than 3 minutes.