It comes down to difference of opinion and what sort of games do you prefer to play.
Fallout 3 continues with Bethesda's game design choice to let players create their own stories, offering them a relatively large and allegedly detailed world to explore and interact with. This is what Bethesda games are all about. They don't go to offer you a hand-crafted experience, they give you the opportunity to make your own. Do they do this perfectly? Of course not. But if you go into their games with the wrong mindset, you are in for a disappointment, regardless of whether or not they have done good work.
In comparison to Fallout 3, the first two Fallout games offered a more hand-crafted experience at large. The world offered only a few points of interest, with random encounters littered across the way, and overall I feel the game was more directed than Fallout 3. This is not a bad thing, but it shows that even open-ended games can vary to different degrees, and I think Fallout 3 varied from its two predecessors quite a bit there.
When I first played Fallout 3, I joined the unsatisfied echoes calling the inadequacy of the game compared to its predecessors almost instinctively, and in spite of my enjoyment of the game. Having recently played Fallout 1/2 I realized, and this realization may definitely be only my own, what happened: I was being nostalgic. Not the good kind of nostalgic moaning about the lack of interesting and well-designed stealth elements when compared to the Thief series. The bad kind of nostalgic where the old games become so over-glorified in my mind that a cup of mud may well as well be remembered as a cup of sweetly goodness (or in the case of Fallout, a cup of sweetly goodness being remembered as the nectar of the gods themselves).
The first two Fallout games were good, even great, and having their memories still fresh in my mind I can more clearly see the fundamental difference that I find between them (and STALKER) and Fallout 3.
I have my share of criticism for Fallout 3 (after all, nothing is perfect unless one is being pretentious about it). Overall, I feel Bethesda has done a good job in capturing the Fallout experience, and I can definitely count it as a Fallout game. I found that I managed to get immersed into the world and experience it the way Bethesda intended for players to experience their games and explore the world to my heart's content, telling my own personal story in the Wasteland (something I never managed to do in Oblivion).
I am not one to argue the difference of opinion, and certainly am not so pretentious as to call a game bad (or good) based on my own opinion alone, particularly an uninformed ones. Like I said, I can call the flaws that I find on Fallout 3, but I would warn against being overly nostalgic or expecting something out of this game that it never intended to give.