I would stop making useless social spaces
I would start killing off vangaurd, and get the factions involved WAY more. I mean missions, story-lines, and attacks
I would bring back Ammo Synths
I would stop making leveling useless. If you go to a starter zone, and are max level, you will curb stomp everything.
More Melee weapons. Also LMG's would be back
Weapons would be broken into 4 classes, Primary, Secondary, Pistol, and Heavy
Weapon upgrades would be completely different. All scopes/ sights would be available for a weapon, all barrel types, all Magazine types, and I would add in Fore-grip, and Stocks. All of them would have to be unlocked through either use, or weapon parts (not sure which).
Shaders would not be lost when used, but keep them as 1 per armor piece.
Those are my thoughts before I get coffee, I might add to this later