Comparing one of the best-written quests of Fallout: New Vegas to one of the more poorly-written ones in Fallout 3 is hardly fair, wouldn't you agree?
If you compare FO3's better questlines and areas to NV's better questlines and areas, say Tranquility Lane and the Pitt, I think Fallout 3 holds its own well enough. It's not as well-written overall, but it's hardly garbage across the board.
Well, I did love tranquility lane, though the Pitt doesn't count because it's a DLC.
To address James, he clearly did that so as to prevent the Enclave from being able to torture him for the information. If he had surrendered, they would have taken him back to Raven Rock and tortured him until he gave up the purifier password. So, in my opinion at least, his actions are perfectly justified within the context of the story.
They likely would have killed him and only realized after he was dead that they needed something from him, judging by the incompetence of the Fo3 Enclave. But the rational thing to do would be for him to just cooperate, he obviously wasn't going to defeat the army of men in power armor who wanted to seize his little project. He put the life of his child in danger by provoking the obviously hostile men. The Enclave let the scientist who cooperated live and stay her Raven Rock to join the researches, and that's likely the fate that would have been guaranteed them all. They would be imprisoned, but also have access to far superior technology to further the project. Doesn't sound like a bad trade for someone who wants to get the project running, and sure beats the alternative situation that he put the others in... realistically, if your character didn't have magical protagonist powers, James got them all killed.
Also, isn't seizing a plant that doesn't belong to you for the 'good of the people' something the NCR would do? Seems similar to me.
As far as the food issue goes, yes, FO3 does not represent where the population gets its food from. But neither does NV; all there are is the NCR Sharecropper Farms and then some small livestock herds. Most of the major military installations have no visible source of food, either, and the sharecropper farms is hardly going to be able to provide for the entire region. Both games gloss over the issue, and I really don't have a problem with them doing it, as it's clearly done for the sake of game design.
No, there is a lot more than that that references where the food and water comes from. The brahmin barons fighting over ranch land, for example, and [SPOILER] Heck threatening a food embargo on the strip. The bighorn ranchers spread throughout the various locations. They address the issue, and it's a really vital issue for a world that's supposed to be a wasteland.
I can also name quite a few memorable characters (for me, naturally) from Fallout 3:
-Three Dog
-Sydney
-Fawkes
-RL-3
-Moira
-James
-Butch
-Eden
-Elder Lyons
-Sarah Lyons
I could just as easily rattle off a list of names that long for NV; both games have their merits.
Three Dog- I'll give you Three Dog, though I don't find him very interesting, he's one of the more developed characters. +1
Sydney- Just and cut and paste mercenary girl, no personality to speak of. +0
Fawkes- He doesn't get much face time, but I'll give a half point for Fawkes. He's good, but underused. +.5
RL-3- It's a shame a robot is one of the 'characters' you mention to actually have some personality and development. I think that says a lot about the state of the human NPCs in Fo3. +0
Moira- Some people find her annoying, but I'll give you this one. I like Moira. +1
James- No, he doesn't have depth. He's a stereotypical dad who has to leave his family for the greater good. The only reason the viewer is tricked into thinking this character has dimensions is because Liam Neeson can make ANY role sound deep and awesome, he's just good like that. +0
Butch- ...Seriously? You put a Stephen King bully on the list? I'm docking credit for that one. -1
Eden- Eden I love, though only because he's voiced by Malcolm McDowell. Like James, I don't know if this really should count, the actual writing is still awful. The scene and performance have an amazing effect, but if you turn the sound off and just read what Eden is saying, it makes no sense. Why is the brilliant super computer of epic evil giving me the key to foiling his grand plan? He has no reason to trust me. An inconsistent character, though memorable.. so I'll give you this one. +1
Elder Lyons- Alright, you've got me here. +1
Sarah Lyons- Eh.. nah, just a blond J. I. Jane. +0
So, in total, we come to 3.5 total characters in the game. You didn't mention Amata, and I liked her character (though a bit bland, still good for Fallout 3), so I'll give a bonus point. 4.5 total, still able to count 'em on one hand.