Whatever overlap you may perceive there to be mechanics or game feel wise don't matter, destiny 2 is not an extraction shooter so marathon is not and never will be "basically destiny 3".
Marathon really attacks a lot of faults of current Destiny.
-Simplified to one game type that can be built upon directly combining a lot of what is in Destiny.
-A system for loot to dissipate, sorry but having a vault of shit after years was dumb plus with the meta changes most of the guns are worthless. That is now built into the game itself through item degradation. Also you dying and losing your stuff makes sense and is interwoven to the story.
-Timed event no more 5-6 hour raid runs, broken into smaller parts. Also values your time meaning you can extract anytime after 5 minutes have elapsed in the primary maps.
-Game will continue to focus on mechanics but the game is focused more on action. Your not running around shouting 48 callouts to everyone. Flappy Bird, Double Fish, etc.
-The PVP and PVE mechanic works having contracts to complete, objectives on runs, while fighting PVE and PVP teams adding more variety than just PVP or PVE separate, you get all of that in one game mode.
-Everything is done from the main menus, you dont have filter bullshit having you fly to the tower to pick up a certain thing or this or that. It is all one place, then you jump into a game.
Look at Bungie's history
Marathon 94-96 single player
Halo 2001- single player and multiplayer PvP only and multiplayer PVE
Destiny 2014-Mass multiplayer PVE and a game mode with mix PVP and PVE (gambit)
Marathon 2026- Mass multiplayer PVE combined with Mass multiplayer PVP
When we say Destiny 3 we mean it is the next iteration of Bungie taking the previous game attributes and improving on them. We know its literally not Destiny 3. Also there will be a Destiny 3 most likely and some people will still hate it. Destiny 3 is a made up game at this time in some peoples minds that fixes the current faults of current Destiny. That version of Destiny will not be made, because it is not simply possible to do. So throwing out that Destiny 3 is the fix all everyone wants is an unrealistic expectation. If you want Destiny 3 to be a carbon copy of Destiny 2 you still have Destiny 2 which they are still working on it.