1. Race Customisation
This is probably the most talked about idea for Fallout 4; we need more choices for our races. We want to play as a Super Mutant or perhaps a Ghoul. Even if Bethesda couldn't make that a reality, we should be able to pick a faction in our character creation, like the NCR or the Great Khans. This would add a lot of depth into the story, because it would limit the choices on who you would choose for the endgame. Bethesda should make it so that a Khan shouldn't join the NCR because they are
enemies. Now, if they choose to do actual different races like Super Mutants or Ghouls, these should be reflected in-game. If there is a town full of Ghouls that hates humans, wouldn't it make sense to have the Ghouls attack humans, but not another Ghoul? This could be the start of another questline, just because of the race you choose at the beginning of the game. Now, there are so many ideas about how races could be implemented, so I look forward to hearing your responses in the comments section below, along with any ideas I missed.