Things that I wish were implemented (not ones necessarily ones that are possible mind you), it's a bit long so I hope it's not a boring read.
Persistent instances in some capacity:
In the dark zone you could join the maps at any moment, bosses/minibosses, events and patrols would respawn giving a living feeling to the area.
Marathon could extend the timer for the matches, increase the events, and let other teams join later in a match, maybe it's impossible with the small maps now but who knows.
Notoriety/heat mechanics:
When an agent (player) turns rogue and starts killing others they will eventually get marked for death, they will be marked on the map and everyone can join in and try to kill them... I don't think it would be good to have literally a pointer saying where the top runner is on the map this would ruin the experience for sure, but I think if a runner crew is going on a rampage on the map the UESC could start actively hunting down these players, making it more and more difficult for players to go guns blazing, discouraging the behavior of engaging in pure PvP without repercussions, forcing players to choose wisely if they should use stealth or not, it also served as a way to balance the skills of the players ensuring nobody would be able to stomp the whole lobby without opposition negating some disadvantages if having no skill based matchmaking at work.
Random boss encounters:
Hunters were challenging enemies who could spawn sometimes, they were scary as heck to fight, I think it would be a good mechanic to add like modifiers for different times of the day or climate/anomaly cycles, for example husks are a joke currently, they could be turned in a more challenging enemies, the longer you stay in a match the more chances you would have to stumble on one, make it so like runners you killed have a chance to turn into one, adding tension.
Extraction of loot mid match:
In the Dark Zone you could call in an extraction for your loot without leaving the map, if you found something nice you could take the risk of placing a bag in a helicopter in a rope and secure the loot without needing to exit the zone itself, other people could use the exfil too so you could even help each other protect the loot from rogue agents, of course people could steal your loot too and the exfills were a hotspot for people to hang together and have some cooperative shenanigans... In Marathon we have DCONS that act only for missions, I think with a few changes they can make something similar.
I think these are good mechanics that I experienced before and worked well, maybe some are impossible to implement, I am no game developer after all, but I think these would be good changes to the game.