Yeah, we should definitely all keep our own nuts.
As for it being "barely an upgrade:"
* The weapon and armor modding system.
* The general usefulness of junk, which grows out of the mods.
* Actual weapon variety - FO3's weapons were nearly uniform, and the Chinese Assault Rifle you picked up early was pretty much the top-tier of the useful-indoors weapons.
* The change from skills to perks.
* The settlements.
* Dog Meat may hilariously set off laser tripwires in YouTube Videos, but trust me, he's far more sensible the suicide dog in FO3.
* The companions in general are on par with New Vegas Companions, rather than the nonentities of FO3. Plus, it's now clear what actions they like and dislike.
* Radiation actually matters now.
* The Pip Boy companion app (may not affect non-tablet owners)
I'm probably forgetting other things.
I think a lot of the problem is that so many of us played FO3 & FONV with mods that often did the same thing, but better. I could modify most weapons, and I started with actual weapons, not the pieces of pipe arranged in interesting arrangements. I could make combat deadly, rather than fighting an array of bullet sponges as a fellow bullet sponge (albeit one with an incredible vulnerability to grenades.) If I tired of companions like Veronica and Boone, I could load even better companions like Sydney or Willow. (Although I will admit that Nick Valentine is probably my all time favorite character model.) I had across the board better character models and animations and textures. I could actually throw a grenade without playing keyboard at a Carnegie Hall level. I had deadly radiation storms and hunger and thirst and crippled limbs that could not be healed until the area had been cleared of enemies. Sure, Fallout 4 is worlds above Fallout 3 or New Vegas as released, but generally it isn't as good as what modders made of those games.
Every improvement comes with an accompanying if unrelated regression. The map is nicely notated but far too small, so that taking cover around one building often brings one into another mob's territory and it can be difficult to find anything in the plethora of symbols. There are great improvements in draw distance, but the textures themselves are far below modder quality. We get power armor very early, but it seldom lasts through one building, at least on survivor mode, so the lack of firearm and armor maintenance in general is offset by constantly needing to rebuild power armor, and this is made more difficult by our inability to mark where we left our junk at the power armor repair station. Seriously, not only do we not have the ability to notate our map (something every Tom Dick and Harry can do instantly in spite of having been raised in a low tech world and never having seen a Pip-Boy) or place multiple markers, but we can't even place our one lousy marker unless it's at a named location. WTF? We have much improved voice acting, but our choices have been dumbed down considerably to yes, no, sod off, and huh? Sure, at times they may look different, but rest assured that what your character can and will say (at your behest anyway) is limited to those four responses. We were given a voiced protagonist to convey emotion, yet no remembered to tell the writers to write emotion. We have total control over our character's face, yet every possible choice looks like it's carved out of dog squeeze by a seriously intoxicated blind man on a roller coaster using a crooked stick.
I am enjoying the game somewhat and I am glad it's doing well, especially since this is probably the last Fallout I get to play, but I can't see me putting in a hundred hours until the modders have had it a couple years.