Alright as promised, I'll post the things that I personally liked about Fallout 3, what I feel it did "right" and why I still enjoy this game, even in the presence of New Vegas (and sometimes in spite of).
Atmosphere
Fallout 3 had a very post apocalyptic atmosphere; more than that of New Vegas. I liked that it seemed people really were struggling to survive as one would expect in a post apocalyptic environment. Life didn't seem too easy for the settlements and the population. You really got the feel of how hard and harsh things are in the wasteland. Then there is the dismal tone throughout, you just feel like every second you stand around, you are risking something nasty finding you! So the atmosphere of FO3, I felt, was handled correctly.
FO3 also FELT like Fallout. It really did, at least to me. It captured the old 50's era really well, with all those protectrons running around, the pre-war clothes, the posters, the vehicles themselves the building designs...it really captured the feel that FO and FO2 tried to bring; you could easily believe that this world ended with a 50s era mindset and (for the most part) tech. That right there, a large part of the original Fallout games' atmosphere, was very well carried over in FO3.
Random Encounters
Everyone talks about how New Vegas is so superior to FO3. But New Vegas lacks TRUE Random Encounters. In FO3, you could run into a Deathclaw right outside of Megaton if you got unlucky enough. Encounters were very much random in the sense of you never knowing for sure what you would run into. Yeah, they occurred only at certain points on the map, but still; what you would find could be anyone's guess, from a wandering merchant to a pair of pissed off Yao Guai.
VATS
It took some getting used to, but I liked the Vats system. I'm glad they did away with the reduced damage during VATS that they had in NV, but the system itself is wonderful. I've found myself wishing for such a system in Skyrim a time or two, when I throw a ball of fire and kill an unintended target (a civilian more than once, damn them!). I also like how VATS used AP, and it was reminiscent of the aimed shots from the old school FO games. A nice way to adapt such a system into a third person/first person shooter. Now, if they just gave you motivation to aim for more than just the head--but this was an issue even in the early FO games, where you had little reason to aim at more than just the eyes. So for me, VATS is another thing that FO3 did right.
Characters
Yes, I said characters. There were a few wonderfully done characters that were both entertaining and likeable. Moira Brown probably my favorite FO character of all. Quirky, fun, and a blast to go on completing her Wasteland Survival Guide. I always enjoyed those quests and the incredibly hilarious dialogue options you were able to have throughout. Then there was Fawkes, who was interesting as a character--not just a clone of Marcus either. And the always good for a laugh Mr. Gutsy. Dukov was a fun character too, as was that scientist when you enter that simulation (I forgot the name of it) while looking for your dad. Some of the characters were every bit as entertaining and fun as those in FO1 and FO2 (if not moreso). I think they did the characters right (for the most part), even if the plot itself was fairly weak.
Weapon selection
So many guns to choose from. Hunting rifle, gatling, the famous gatling laser, plasma rifle, .32 pistol, Fatman, laser rifle, Super Sledge, Assault Rifle, combat shotgun...There were so many damn guns to play around with in this game!! My only complaint is that alot of them were inferior to the first two weapons you are likely to get: your 10mm pistol and a hunting rifle. Those two can get you through a good chunk of the game, then you can move up to the combat shotgun and AR or Sniper Rifle, and as far as small guns go, you're good the rest of the game. Still, regardless of how useful the different guns were, you had a LOT to choose from, and they did that damn right. Many of them were amazing versions of the old FO games too--I was especially impressed with the Plasma rifle. I think they improved that one, it uses a Big Gun animation in FO2; I'm happy to see it looking like what it is in FO3 and NV: a RIFLE.
Enemies
There was a nice selection of things trying to kill you, some old and some new. The Deathclaws were BADASS, exactly how I would've imagined them to be from the old FO games. A little disappointing you didn't see packs of like 20 radscorpions but then again, as strong as the giant variety were in FO3...you wouldn't *want* to deal with more than a couple at a time, and even that was a pain in the ass. Then you had raiders, molerats (the small variety), ghouls (Feral and non-feral)...and the brand new Yao Guai. Could there have been more enemies? Sure, but then again, the wilds were filled with them with the ones they had. Always felt dangerous, venturing out, especially if you were going into the mountains!
Exploration
A large part of FO1 and FO2 was exploration. This only became even more emphasized in FO3. With the first two games, there was a SHITLOAD to find if you took time out to go off the beaten path. FO3 continued this tradition, not only with special encounters but also interesting places (especially in DC), and they also provided a lot of backstory to things that other games would've ignored. What comes to mind is the farm with the destroyed grain silos and the computer. You learn about the family there, whom were slaughtered by raiders. This is NOT necessary info for the FO universe, they were just normal people--but it was included anyway. I could site probably a hundred examples of such bits of information about the world. They weren't necessary for the game, but they added to the overall post-apoc feel, AND they gave you something fun to come across while scaving the wastelands and brought life into the world around you.
Was Fallout 3 perfect? No. It was glitchy as hell at times (where the f***k was QC?) it had holes in it where it comes to lore (they were remaking a game how many years old? Could they have been expected to get it perfect??), there were a few gameplay hiccups and there weren't a lot of really meaningful in-game choices that really felt like you had all that much impact on the world around you. There were some, though, enough to still provide that FO feel, but it was lacking enough that sometimes it felt like your choices weren't really making that much of a gameplay difference. Still, there were some satisfying dilemma's too. But I'm getting sidetracked. Point being, yes, there are imperfections in this game, but FO3 did plenty right, and brought plenty of cool, new things to the Fallout Universe that could be called an improvement--or kept to the spirit of the original games. The points above are why I thoroughly enjoy Fallout 3, and I could even go so far as to compare it to New Vegas if I wanted to, and why I prefer 3 over that disappointment--but that's for another topic.
SORRY for the long winded post *whew*