1: There are roughly 8 times as many Workbench recipes, plus a Campfire(for food and consumables) and a Reloading Bench(for making bullets). Crafting is expanded to include a large number of otherwise rare & valuable items, such as Atomic Cocktail, Nuka-Cola Victory, Antivenom, & even Stimpaks.
2: Less "flashier" guns, and more better thought through and balanced ones. Fallout 3 definitely has the more "explodey" guns, such as the ridiculously common Fat Man. However, unique variants of weapons have unique textures & usually have features which make them perfect for certain styles of play. For example, the ubiquitous 10mm Pistol is rebalanced from a starting weapon to a mid-game sidearm, generally deadly against unarmored enemies & quite lethal with a suppressor. The unique Minigun, Avenger, fires faster, deals more damage per shot, is more accurate & weighs less, but it only carries 120 bullets per magazine instead of 240. Whatever you're looking for in your specific combat style, you'll find it.
3: There is more clothing and equipment, but for the most part the existing clothing and equipment have been made more useful. Armor now provides a real level of protection, alternate ammo types allow a Guns or EW specialist to achieve new levels of lethality, poisons help Melee/Unarmed players stay relevant, and purpose-designed consumables exist for different situations, such as the Super Stimpak(which heals 2.5 times as much as the Stimpak) & a drink that causes you to take less damage from fire & energy weapons.
4: The new weapons are significant if the character invests the skill into using them well. An Assault Carbine is worse than useless in the hands of a pure Energy Weapons character, but that same carbine is an end-game weapon in the hands of a Guns specialist. There is no weapon that you "have" to use to beat certain adversaries, and no weapon that you'll find yourself progressing to as the culmination of that weapon skill.
5: The ending system gives you an individual slide for each companion, town, major faction, your karma level, your allegiance, and for a lot of the quests. There can be a total of 27 slides. I feel it closes the game better.
6: Companions now have opinions. Which they will voice, and they will proactively leave you if you trample on them. Companions also each have a quest that ends with an improvement to the companion in some fashion & with the feeling that you're helping them close off something in their lives. I feel companions are more meaningful this way. On top of this, there is a "companion wheel" which allows you to trade items, administer Stimpaks, and do everything short of firing them or talking to them without talking to them.
7: I am not qualified to comment on the game's bugginess. I can merely say that FO3 is buggier for me on my PC.
8: Almost every quest stage can be altered by the player's action(or lack thereof). You can even fail main quests, though there is always a path to ending the game. Were the James death scene redone in FO:NV, the PC would be able to hack their way into the thing with a high enough Science skill, and take on Colonel Autumn to protect their father...or to shoot their father and join the Colonel.
9: All DLCs add, at a minimum, one of each type of weapon, several armors, and a few perks. From a quest standpoint, no, not all DLCs have equal amounts of quests. Lonesome Road is very linear with a small amount of quests, Dead Money has a lot of exploring with a moderate amount of quests. Honest Hearts features multiple quests & sidequests, not all relating to the plot of the DLC at all. However, every DLC's quests fit the DLC perfectly, and offers rewards beyond quests.
10: In most every situation, your character can say whatever she would say, and get a reasonable reaction. You're not going to run into an NPC who you refuse to help and which they reply to "Ok, come back when you change your mind." There are two situations that come to mind where you can't just say whatever you want: Talking to Yes Man, and the initial meeting with the protagonists of Old World Blues.
11: Yes. Reputation controls what each faction thinks of you and whether they shoot at you, whereas karma is used on a personal level with some characters. NCR doesn't care what your karma is, they're only going to fire on you if you go around shooting their soldiers.
12: I would say yes. There's something for each character, including the ability to say "Screw them all!".
-Nukeknockout