Honestly, I don't want Obsidian handling Fallout exclusively as the problem with New Vegas was it relied too much on nostalgia and after the remake in Fallout 3 of F1 and F2, I was looking forward to more new material with Bethesda handling the East Coast and Obsidian handling the West Coast. I wanted to see parallel development and see how they were handled.
Here's a list of things which I think would have benefited the game.
1. Revamped Conversation System
Pretty much I don't care for the Mass Effect-style conversation wheel, which is odd because I think Mass Effect did it fairly decently so this is Mass Effect but worse. The mod where you know what you say is much better. I would also add about 20,000 more lines of questions and answers given I feel massive amounts of lore were left out.
2. More Cities, Less Settlements
Fallout 3 basically had Rivet City and Megaton while Fallout 4 has Diamond City and Goodneighbor. I would have appreciated if they removed most of the generic Settlements and then replaced them with actual locations which might be interesting to visit. Vault 81 was a great quest but I wouldn't mind actually making it a hub.
If you were to remove the massive amount of wasted settlement space, you probably could have inserted Far Harbor and Nuka World into the map.
3. Restore Missing Content
The Combat Zone, the Robot Race Track, Paladin Danse overthrowing Arthur Maxson as Elder of the Brotherhood of Steel, and other material which we've since discovered to be missing like the Underwater City (Vault Deep 6?) seem like they would have done better to have been incorporated into the game.
4. Raiders as the 5th Joinable Faction
This is just the obvious one which has been repeated from the beginning but the option of joining the Gunners at the beginning would have done a good job of satisfying those who wanted evil content. I think everyone wanted the option of having Raiders blow up the Institute or the Prydwen or both.
5. Make Goodneighbor a rival hub to Diamond City
I think they could have made it about four times as big. As is, there's a lot of allusions to Goodneighbor like the fact it's the Triggermen's home base and a wretched hive which it's too small to deal with. I would made Goodneighbor built over the Triggerman's Vault if I were doing it and have it also be a place of chems and villainy.
6. In the words of Bruce Lee, Emotional Content
If we're going to go with the fact you're a father or mother looking for your child then bestow the option of actually having the Sole Survivor fucking emote every now and then. He's basically Dinklebot. If it would APPALL players, maybe mark it as a Special Blue Option or something.
Some moments to show emotion:
* Talk about Spouse and whether you loved them, were going to divorce, were ambivalent, or whatnot.
* Confronting Shaun about the Super Mutants, murder of surface wielders, and massacre of settlements above.
* The option of sparing or executing Kellog.
* The option of talking to your romanceable companion about your marriage to your spouse.
* A chance to talk about the Pre-War world and how much you hated it or loved it or miss it.
* Talk about why you joined the army or not. Both SS should be veterans, IMHO.
* Special dialogue if you give your companion your wedding ring and the option of making new wedding bands or buying them.
* Special Dialogue if you're in a romance and make a crib.
* Asking Shaun about who raised him to be such a murderous psychopath or what his goals are, really.
* The return of the Gay Option Perks for Special Perks as well as Lady Killer or Femme Fatale.
7. The Boston Tunnel System
It's absence is rather noticeable given the focus of Fallout 3 on scary tunnels.
8. More Quirky Sidequests
There's a lot of good sidequests in the game but I swear, they're damned spread all across the map when they should have at least one major one for every major location.
9. The Kennedys
Honestly, I think their absence from the game in some form was kind of disappointing. I think it would have been fun to put a ghoul family in a destroyed mansion for missions like that. Either that or drop the majority of the Lovecraft stuff to make the Cabots to be their equivalent with them living lives of luxury PA versus worried about immortality as their quest focus.
10. Faction Choices
Because you come to lead so many groups, I'd do the following:
* Have the option of freeing the Synths after you defeat the Brotherhood of Steel as the Institute Director.
* Have the option of presenting a treaty to the BOS or Railroad from the Institute even if they refuse it.
* Have the Railroad, once it succeeds in its mission, refocus itself to freeing slaves all across the East Coast.
* Have the option of formally allying the Minutemen with one of the other factions.
* Free the slaves of Nuka World if you win.
You know, so you don't feel like you're having no effect.
11. Ending Slides
Does anything more need to be said?
12. Two more Expansion DLC
The first off the top of my head would be Doctor Zimmer and the Lyons Pride in a fun homage to mad scientist stories. It might be a little too similar to Automatron but I still think it'd be a fun Easter Egg filled story for those who loved the Capital Wasteland. The second one I would have involve the Enclave but we can never get too much of them.