There's a difference between handholding and bullshit.
There's a handfull of Very hard and hard safes and terminals in locations that are very reasonable to assume you're about level 5 in. Metro on the way to GNR or Rivet City, etc. At no point in the game do you have any reason to backtrack to those locations. The rewards are inaccessable and may as well not be there.
'Has no reason to exist' can be applied to just about every sidequest in every game ever, so long as it doesnt directly impact a main character. In terms of illogical motivations, I fail to see why you bring up Beyond the Beef, which makes perfect sense to me. You have a bunch of cannibal tribals who were offered a position of power by House, and through that, they continue to practice canibalism. They kidnap the kid of a tourist to eat cause that's what they do, and from there the quest starts.
I can pull up a number of quests in 3 that i've gone 'well that's a stupid quest',
>stats killed replayability
Nah, it allowed players different ways to go about finishing quests that were tailored to your character. FO3 is primarily 'go here, shoot some guys/talk to some guys, go to another place, shoot some guys, talk to some guys'. There are very few skill checks, very few alternate paths of completing the content. FO3 really likes its gun fights, but the engine has ass gunplay, so at times it gets tedious.
>linear skill checks are bad
The implementation is good, specifically because instead of optional rewards, the player is using their skillset to advance quests. This ties into my last point. FO3's quests are guns and speech checks. NV's quests are all over the place. For this to work, they have to be somewhat linear.
>npcs talking about things is depth
Obsidian opts into 'show don't tell'. Bethesda goes for exposition dumps, and while at times it's pleasant to know what the fuck is going on, having a player lack knowledge is a powerful narrative tool.