Ah I much prefer the main quest in Fallout 3, in fact I just like the game better than New Vegas in general. Apart from a couple of things I'm almost a walking encyclopaedia on Fallout 3, whereas on New Vegas I've only really played it through a couple of times and scratched the surface. It just doesn't do it for me, I think it's the Mojave Wasteland more than anything. Don't get me wrong, I love them both and they're two of the best games I've ever played in my short life but the Capital Wasteland is way better for me.
Better scenery, better landmarks, more places that are recognisable like the Arlington Cemetary, Washington Monument, Lincoln Memorial and then the places that you can see from miles away like Tenpenny Tower. The only things that bug me are the metro tunnels but once you get used to them they're okay, though I was happy to see the back of them in New Vegas.
I also think Fallout 3 has much better weaponry. The custom weapons that you can build in Fallout 3 are all epic, don't think I built a single one in New Vegas, in fact I don't think the game even has the schematics to do so. I know you can buy parts and modify your weapons but it's just not the same for me. I loved finding all the individual components and then seeing how they fitted together on the weapon, and how the weapon worked. Some of them were absolutely devastating like the Dart Gun which instantly cripples legs and starts draining HP, even better is the damage stacking per dart.
It's little touches like that which make Fallout 3 better in my opinion and I also really loved all of the DLC's apart from Mothership Zeta which felt like a monotonous corridor fest. Point Lookout was really impressive as a DLC and it was definitely worth the money, also I loved The Pitt and the whole industrial-ness to it. It felt really eerie and not a nice place to be which is an epic achievement for a game to give that kind of feeling to me. Broken Steel was good, but short, though I loved some of the weapons that it added like the Tesla Cannon and then of course you get to see the after-effect of The Purifier with some of the quests like The Amazing Aqua Cura and the various caravans distributing the clean water throughout the wastes.
The thing I love most about Fallout is the attention to detail. Like in The Amazing Aqua Cura you've got the Ghouls selling dirty water but claiming it's a miracle which can restore hair. Pickpocketing Griffon shows he's just wearing a wig and selling the dirty water at high prices, I just love the little touches like that. They really make the game something better than your average thing.
It's the same with the weapon schematics, you can really see how each component makes the weapon, the surgical tubing acting as a rubber band to fire the darts from the Dart Gun for example, or the motorcycle handbrake used on the Shishkebab. Sorry for rambling on, but I could really talk about Fallout 3 all day.