Really? It seems fairly obvious to me what the biggest and most common determining factors leading to a preference toward FO3 are:
1) FO3 is your introduction to the series (people don't know if atmosphere, tone, humor, gameplay, characters and factions are missing the mark if the missed mark is their starting point).
2) A preference for sandbox, open-world exploration games more than traditional RPGs (TES fans).
3) Enjoy action more than dialogue (FPS fans).
4) A preference for god-mode over specifically built characters (i.e. wanting to do all things, all the time, instead of being limited by skillchecks and stats).
It's easy to tell that you're from NMA. I think of the four reasons you listed the first is perhaps the closest and most common. I can probably expand a bit:
Atmosphere:Fallout 3 really pushed the '50s feel. It was the baseball, white picket fence, "american dream" type of feeling. The idea that the cold war happened and you were now living in this ruined, post-apocalyptic '50s type of world (I am aware how this was different from F1/F2). One radio station played iconic '50s hits from Ella Fitzgerald, the Ink Spots, Bob Crosby etc. The other played patriotic American propoganda. You live the first part of your life in an isolated vault-tec vault, with it's comfort and isolation but cold bulkheads and bright lights.
When you emerge, the game world itself is dirty and rusted. The trees are scorched and the earth is barren. The combination of introduction, design, ambiance and music give you the sense that "this is a wasteland" and that the atmosphere has an undertone of the 50s/coldwar era. Even the quest fade in text crackles with a geiger counter sound effect.
New Vegas, like F1/F2, did not push the '50s feel. To be honest, I can't really speak to what feeling they were pushing, if any. Country I would guess? You spend most of your time in the Mojave. The introduction doesn't say much about the war but focuses mostly on the factions and Benny shooting the courier in the head. Even the music at the end of the intro when "Bethesda Softworks" appears is enough to give some pause if they were expecting more emphasis on a '50s/rat pack type of feel.
I believe that is the atmospheric difference most people notice. That's of course in addition to it no longer being a post-nuclear wasteland but something that seems like an "old west" desert full of cowboys, the music being a completely different style and etc.
It is easy to tell that Obsidian designed this game and not Bethesda, because they prefer to tell you a story while Bethesda tries to make you feel it. How someone absorbs the atmosphere, whether through dialogue or other means probably makes a huge difference in which game they will enjoy more. Myself, I would probably rather have a "C" grade story with an "A" level atmosphere than vice versa.
Humor:I probably can't speak to this because I don't find many things funny and the whole thing is entirely opinion based. Some people think Fallout 1/2 were hilarious but all I saw were toilet jokes, pop culture references and dialogue options that broke the fourth wall. I didn't really find Fallout 3 that funny either, but chuckled at things like Moira Brown's inane survival guide quests and the chick with the Nuka-cola obsession.
I have seen in NV the increase in "inappropriate" dialogue options or the ability to choose a text that seems really random. I would assume this is the humour people were looking for. This probably isn't a huge deal for most.
Questing:I've had the chance to talk to a few real world friends who've been playing. We've come to a general concensus that there is an overwhelming number of both quests and dialogue in the game. A level that seems to be almost inconsumable. This has been a detriment to the experience, in that a great many of the quests (not all of course) are extremely tedious, dialogue heavy or fedex quests that consume a lot of time for little pay-off story or "reward" wise. Even some of the most necessary quests, like getting the power armor perk from the Brotherhood of Steel, drag on needlessly and take what seems like hours to complete.
And it's not just that quests can be tedious, time consuming or what have you... that exists in Fallout 3. It's the manner in which there are so many of these and that everything is so intertwined with the main story that you can't seem to get away from it. The comparative anology I have arrived at is the following:
Fallout: New Vegas is a 12 course meal, every single night. It's great if you're hungry, but if you're not the quests can be so large, tedious, and inconsumable that you may stand up from the table shortly after sitting down. I've heard more than a few grumble about replayability, not because the story is bad, but because they don't want to get reinvolved in a labyrinth of quests they don't want to do. About 20 hours into NV I was actually starting to feel like I was playing F2 and it was displeasurable.
Fallout 3 is a buffet, where everything is separated and compartmentalized into a pick and serve kind of format. This may be because the main quest is so de-emphasized or because many of the side quests are uninvolved. It's hard to say, the quest structure and what the quests have you doing seem to be laid out entirely different.