i think there are a lot of reasons why Fallout 3 is such a great game such as:
1) Meaningful exploration: Fallout 3 was a large place (which should be a given) and like in many rockstar games, the location is often can be a character itself. Also in Fallout 3, the exploration was worth the travel because there was a 90% chance that a unmarked sidequest (that you actually wanted to do, unlike in its successor) would happen and you would enjoy it, or it would have something meaningful for your travel.
2) Fallout 3 plot never got too big or complicated for its own good: The plot was pretty simple compared to other games where developers would take a big leap in storytelling or complex plot that more often than not, it crashes and burns,leaves the player confused, or maybe the player just wont care anymore. Bethesda played it safe by having a small story that people could more than likely relate to in some way and care about the outcome of the game. many people including myself all remember taking a vow to absolutely destroy the enclave after they killed your father james in project purity. There are very few games such as the Mass Effect series where you can spend ages deciding on a simple decision because how it they know that decision will impact the world they inhabit forever. Fallout 3 is one of those games that gets you emotionally invested and care about your decisions.
3) Karma is a female Dog: Like i said previously Fallout 3 is one of a few games still today that made you pause and think of the outcome. I remember the first time i played fallout 3, i hesitantely nuked megaton for the need of cash and a place to crash. After i nuked it, i went to ground zero eventually to see my glory. What i saw made me regret the decision to nuke them, because i felt that the world had suddenly become a lot more emptier than it was before, and immediately went back and decided to save the town in previous save file. One of the many reasons why i found it hard to commit crimes agianst people was that i realised the value of humans (the ones who wouldnt start shooting me on site) because i knew they were essentail to my survival.
4) Memorable DLC: Even though Point Lookout and Broken Steel are pretty much the better DLC of the five, the rest was still worth all the money i paid with it. Though they other 3 were lacking in many of the freedoms in the superior 2, they still did a good job of feeding that addiction to play fallout 3, because they were different from main story, had cool stuff to collect, DLC was filled to the brim with cool things, and after you completed it, you could hardly wait till the next piece of DLC arrived, I'm still waiting for the next 6th piece of DLC to come out for Fallout 3.
These are many of the reasons even after playing games like Metal Gear Solid 4, GTA IV, Uncahrted 2, Red Dead Redemption, and Mass Effect 2, i can still come back to the game and play it like it was my very first time.