If i had to list the top 4 major things i'd like to see reworked or added, ordered by priority, it would be :
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Long term progression of any kind, the more the merrier. Hideout upgrades, passive skills, any long term character improvements.
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Significant cutdowns to the amount of prestige points required in order to get maximum vault space and hangar space. At most 10 for all (or 90% of of all) gameplay affecting prestige persks.
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Incredibly rare items, weapons and gear.
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More random and player driven encounters in raids.
Let's go by my reasonning for each of those points, to see why i perceive them of such high importance :
Long term progression.
This is something that currently separates marauders from older extraction shooters and the recent wave of new ones we've seen flood the market. Arc raiders and tarkov are a great example on why these mechanics are necessary for the longevity of an extraction shooter.
Simply put, in order to incentivise me or most other exfil shooter players to interract with the gameplay loop, you either need many stepping-stone upgrades that keep you engaged and feeling like you're improving your odds with each run, an incredibly immersive gameplay experience that makes you interested in discovering the game's story or universe, or an incredibly crisp and fun gunplay experience. On average, you need at least 2 of those and marauders currently only really stands out in the gunplay, but primarily due to it's uniqueness within it's setting.
Marauders only really has the prestige system and some basic trader missions. Even if we put it's flaws in terms of an extreme grind aside, that is much less than tarkov (hideout/passive skills/traders/prestige/player driven economy and achievements) or arc raiders (skill tree/town upgrades/hideout upgrades/trader quests).
Prestige.
This one is very simple, the amount of prestige points required to obtain all of the long-term progression from it is - a little absurd... well a lot absurd actually. This may be anecdotal, but as a player, i want/expect each prestige to give me...something. As it stands, some of the later upgrades can take as much as 5 or even 8 resets before i feel like i am progressing. That is WAY too much. I'd want to see each gameplay-affecting prestige upgrade to be fully unlocked by the 10th prestige. If you want players to be interested with this system more beyond the 10 or so prestiges it would take after my suggested rework, you can entice them with skins, voicelines, character portraits and more. That will not entice everyone, yes, but you have to consider how many people even hit prestige 10 in the first place in it's current state.
Incredibly rare items, weapons and gear.
This one is also simple, i don't experience the rush of an extraction shooter enough compared to other exfil titles. If i find a gold bullion, i do feel nice don't get me wrong, but it isn't nearly as sweat-shower enducing as finding a red labs keycard in tarkov. You can really get creative with what you'd wanna add. If you consider something like the china lake op, you can make that so rare that seeing one causes a seizure, which would balance the negative feelings associated with dying to or hearing a grenade launcher with "damn that guy has balls, i could have taken the thing from him".
More random and player driven encounters in raids.
This is yet another tarkov/arc/marathon inspired opinion. Player-driven events do exist, you could consider vaults, the asteroid mine's depot puzzle and the warden spawning puzzle dynamic events, but the more of those you add, the more it will vary the gameplay, keeping it fresh over a longer period of time.