1) Like Fallout 1 and Fallout 2. You should make it where the main protagonist in Fallout 3 is related to the main protagonist in Fallout 4 which leads to an awesome back story for the both of them. For ex... Let's say the Fallout 4 protagonist is the son of the Lone Wanderer (Fallout 3 Protagonist)... The mother died of cardiac arrest while giving birth to The Lone Wanderer so you can make it where the mother of the Fallout 4 protagonist dies too, like it runs in the family or something. I don't really recommend that but it's just an example.
2) Next i think you should do what you did in New Vegas, add the NCR and make the Brotherhood just coming out of hiding since they where at hiding in New Vegas. The NCR played a very important, yet interesting roll in Fallout: New Vegas. Their armor, just AMAZING! I just love how you guys added them, as they were in the older games. The Brotherhood where cool in F03 but you made the NCR show who's boss. But I kind of felt bad. The Brotherhood was a strong faction, they even showed the Enclave a thing or two. So, you should make them have a come back and try to actually have something to compare to the NCR.
3) I saw that there were lots of unique weapons, you already do a good job of those, Oh, Baby! (Unique Super Sledge Hammer)
was just the most terrifying weapon I've ever had. I can hear the treacherous screams of my opponent as I clocked him in the gut. The only thing you should guys do though is add abilities for V.A.T.S Like what you did with some weapons. But instead you should add it to all weapons, and/or make a mod that adds it to a weapon to the least.
4) Deathclaws, Cazadors, Nightstalkers... They proved themselves to be very nasty and devastating opponents. You should make a new creature with strength unbelievable that it'd even make a Deathclaw scared.
5) I liked how you added modern weapons as well as new and very technological weapons so advanced even we can't them build today with our technology. But you guys should try putting more Old World weapons, I know people might think it's corny but that was a pretty interesting vibe in the DLC's of New Vegas.
6) Pip Boy 4000? Pip Boy 3000 is nice, but the other Fallout's had the Pip Boy 2000. It'd be nice if you guys upgraded it, since I hear this is your last game. You should add more info on your character, not just health. I think in the Pip Boy you should add an X-Ray. So that you can see how the bones look like when a part of your body is crippled.
7) More Cool perks. I loved the perks but I think you should add more. Like one where you can have no falling damage because it's very annoying when you just beat a mission and forget to save, then you slip over a cliff and die.
8) Last you should add Dual Wield. The player should be able to use any weapon, or two of the same weapon in both hands. It should be a mod for pistols and sharp weapons like knives or machetes. I saw lots of games that had that and they were very brutal to an opponent. It causes more damage, and it is more gory.
Well these are my suggestions, thanks for reading my post!