Its a long list I know, don't make comments saying "TLDR" or "Too Long"
Make the story more personal
the best part of Fallout 3's story is that it is about something everyone can relate to, leaving your safe zone. you leave your safe zone to find your Father, as I am sure most people care about. they even referred to him as "Dad," and have some fantastic writing on his behalf, making him actually seem like the Player Characters Father, and not some random NPC (plus Liam Neeson has an awesome authoritarian voice)
It was very simple, but your small quest ended up escalating into one of dire urgency
Fallout New Vegas' story on the other hand, was one of scale rather than depth, it was difficult to give value to the factions as each of them had nothing but boring fetch quests (Thats right NCR, I'm calling you out!)
The scale was also a bit unsettling. It started out relatively simple, but was blown out of proportion way to quickly, and when It finally did escalate, it spent way to much time on preparation quests, which were copy-pasted for each faction.
There is nothing wrong with a linear story, when you try and break it up too much, every aspect suffers from it.
Some other things that need improvement:
You NEED to have a city section, AS WELL AS a wasteland section. New Vegas' environments get very old very fast
You need to top the Fat Man. The Fat Man was a big gun that shot Nukes, seriously, how the heck do you top that? the Automatic grenade Launcher did have the same "Wow" factor as a small mushroom cloud and the camera shaking like an earthquake had just gone off.
Enough with this "Civilization is rebuilding" stuff, I played Fallout 3 to scour an empty city for supplies, to then dump my glorious pile of loot onto the shop-keepers lap and take my reward, not to walk through 100% colonized areas or areas filled with annoying animals
There needs to be a "Growing up" section. I know everyone seems to hate that part, trying to rush through it as quickly as they can, but that part built precious immersion and pacing, and made the wasteland seems a hell of a lot more dangerous. It doesn't even need to be in a vault, there are plenty of neat ways to do that segment.
Recognizable landmarks are Important. Remember the Mall in Fallout 3? Remember seeing all of those landmarks desecrater and turned into ether a warzone or some kind of shelter? That carries tons of emotional weight. Hoover Dam ALMOST did this, but the lazyness of the interior design ruined that possibility, it looked ABSOLUTELY NOTHING like the real Hoover Dam!
When it comes to weapons, Less is More
In Fallout 3, the cycle of weapons went:
10mm Pistol, Hunting Rifle, Assault Rifle, Combat Shotgun, Chinese Assault Rife, Laser Rifle, Plasma Rifle
that was it. It made the introduction of a new weapon exciting. In New Vegas, there were so many weapons thrown at you at one time, it was really hard to get excited for the "new gun"
Make Followers able to contribute to more than Combat.
so far, the interactions outside of combat have been small, sure there were quests and some dialogue, but the followers never really felt like People. Have them give insight to alternative options to objectives, have specific skills liks bartering for example
Lets say that you have a Barter Skill of 50, and your ally has a skill of 75. you bring this person with you, and they will help you get better prices!
or maybe hacking or lockpicking. Keep in mind, this does not mean that the NPC will do the work, the player should still have to do it, and have the NPC simply supply the skill to do it.
Weapon attachments and special ammunition are a BAD idea.
If I am in the middle of a post apocalyptic wasteland I am not going to find extended magazines for weapons, nor will I find Incendiary ammo. If you really MUST have attachments, make them craftable ones made of every day objects, like a laser sight made out of a laser pointer and a fusion battery
Loveable radio Icon.
I don't even remember the name of the radio guy from NV, but I can recite every word that Three-Dog has said.
The ability to repair weapons without a second one.
Perhaps the player could be able to clean the weapon, or bend broken parts back into shape, or even craft new ones out of scrap Metal.
the ability to cheat combat
Perhaps a player with 9 Charisma would be able to convince Assassins that they have the wrong guy, A player with 9 strength can tell a group of wanna-be raiders not to mess with them. Not every battle could be avoided, but just a few.
Traps
remember all the traps you saw in the game, bear traps, tripwire grenades, stroller bombs?
why Can't I make a few of those?
maybe in certain spots, traps could be made to prepare for a battle, to thin the enemy ranks without having to lift a finger.
NPC interaction (mostly followers)
A loyalty bar?
friendly fire lowers it, yelling at them lowers it.
Taking them out drinking increases it, talking, or working together increases it.
Non- sexual Romance (also follower related) There could be talk of sex later
Say for example that your female follower's friend was killed in battle and she is weeping over their body, there would be the good, evil, neutral, and romantic option for response. Pick enough romance responses (none of which will be highlighted or pointed out), and according to that follower's personality, and they may fall in love with you. develop this further, over the course of the game, and you can get what you are looking for.
This way, the sex scene will seem less tacky, as it would require almost an entire game of development to reach it. (a SFW and NSFW option would be in the menu)
Ok, my hands hurt, i'm going to stop typing now