Alter the Morality System, it shouldn't lock out parts of the game
This increases the number of things you did in the game in a single playthrough, therefore reduces replayability and makes it more boring. In fact, more parts of the game should depend on personal choice. Would be a bad thing to do, at least from the perspective of a RPG fan.
Organic Leveling and Skill Progression
I haven't played Skyrim, but complicated skill systems with many possible choices are always nice (though the skill system used in Fallout isn't complicated, but it would work nicely if every skill is worth spending points on, because you can have tens of very different possible characters, especially having in mind perks, unfortunately it doesn't work in this way, because most of the skills/perks aren't worth it), it also increases replayability, and a title called "Fallout 4" needs replayability. However, the system that forces the player to use certain skills in order to increase them is horrible for a Fallout RPG. Would I have to talk to random people in order to increase my Speech, or will they remove it, because it can't be practiced without forcing the player to make speech checks? What else, make it a first-person real-time shooter? Oh, wait. Anyway, there isn't a strong connection between what are you planning for your character (for example, high lockpicking) and what are you doing - a character with a certain level of lockpicking should use it, no matter what are his plans for his lockpicking skill. So, it's basically a system that limits your actions to what are you planning with your character and makes some of your skills mostly unusable. Not fun. Oh, I forgot to mention that it feels more organic and allows you to better embody the character you're playing as. I guess that by "allows", they meant "forces", because you can do that without a shitty system, forcing it to do it.
I don't care too much the aesthetics of the world. It would be probably nice if they include more colors, as long as it's in a 50s high-tech way rather than a magical way.
An (Even) More Non-Linear Affair
I agree that the world should be more non-linear. I can't say if the beginning at Fallout 3 was too bad, because it forced the player to follow a certain path - it was some sort of an introduction (btw I remember how fast was it to give me the impression of a stupid game, because the player didn't had any doubts in killing a guard from the vault, and the guard was going to kill him as well, for no real reason) and I'm not sure if the implementation of the idea of Vault 101 was possible without it. I'm neutral about this one, Fallout 3 was linear enough (maybe it needed more quests and more content to some of the locations).
Sounds nice. I don't care too much about this one.