It seems to me that part of the reason I burn out so quickly in this game is repetition. Honestly, for this reason I love getting invaded, because though there's no way the stalker can possibly give me anything I want, it's nice just to have something unexpected happen. None of these suggestions are fully thought out, but I think they can at a minimum illustrate that there are so many ways that missions in game can be made more engaging.
Relic Shrines. Fissure missions are really dull. I hate doing them, but I need forma blueprints and ducats from time to time. I think we should always have a relic equipped in any mission. Then we can have an ayatan altar or some such in the vein of a D2 gem shrine that occasionally appears and allows you to spawn some corrupted. You can even put them in some of the inaccessible stations in Railjack.
Next, turrets. It seems to me like finding one should be something to get excited about. In practice though, I just destroy them so no enemy gets inside and is annoying to shoot. How about just axing damage from them entirely and setting it to a % value. One shot does 25% of an enemy's health. If you worry about them being overpowered, they don't need to pivot so fast (so allies will need to cover your flanks) and they can also adopt the railjack overheat mechanic.
Containers! The only time I ever open them is when I'm really strapped for energy or ammo. Fundamentally I don't know how much the looter part of the game really belongs in its current incarnation, but how about letting us rip one of these bad boys off the wall and chuck it for damage? The same for exploding barrels. Perhaps the input can be holding the interact button? Some part of me wants updated loot tables for containers, but I also worry that doing that might incentivize running around the map opening containers, which isn't really what anybody wants.
Treasure Hunts. Mercy killing an enemy with a parazon has a chance to spawn an upgraded reward in a container somewhere on the map. A kubrow can lead you to it, or you can follow a trail you can see with your scanner.
Mutagen cysts. Similar to the ones you have to destroy to kill the hives, these are out of easy sight on infested missions. Taking one out gives a nice buff to your team for the rest of the mission.
Corpus reclaimers. Vulnerable slow moving vehicles that can be driven over bodies to produce valuable resources. Keep it alive as long as you can and turns waves of baddies into grofit!