i think the reason alot of people were upset at the ending is becuase they felt the ending wastn big enough, fallout 1 and 2 had very epic endings, which took alot longer to reach, so this made the player much less likley to be upset because the story wrapped up very well, and in fallout 3 i always thought that the main plot wasnt very driving, i never felt like what i was doing made a difference, and i never really felt that there was a reason in the plot for conflict, the enclave just kindof came in. if the ending was more "epic" than people would have been alot less upset
Its not really a question of being "big", Fallout 3 storyline is simply awful.
To start there is too much of a focus on "Father" that makes no sense (serious, I keep getting incist vibes with the whole deal) as there is no reason for the Lone Wanderer to care, then we get the Purifier that is ... well, USELESS but its made up to be some kind of big deal as the Enclave with their advanced tech go there and grab it for NO REASON (and dont give me the whole FEV virus that is rehash of FO2 plot and put on the last time for the sake of a EVIL option) and we go look for the MAGICAL GECK and it ends with having the YOUR DESTINY being turn on the machine and DIE FOR THE SAKE OF THE PLOT when its possible to have someone that is supposed immune to the thing.
In the end in Fallout 3 you do NOTHING WORTH OF MENTION and die, following "the example of the father" with a nonsensical, poorly researched plot.
Now lets look at FO1 ... the plot does not force the Vault Dweller to do anything, sure there is the Water Chip but you have plenty of time and there are logical reasons to want to wrap that quest up (the Vault is MUCH BETTER that the world outside), then you stumble upon the Master and considering the option was becoming a Super Mutant ... lets say you had a LOT reasons to not do it (and you can BTW).
Then FO2, you get thrown into looking for a GECK since the village is dying and you can ignore it (and I do mean it) and then stumble upon the Enclave and their plans to KILL YOU along with everyone else since you are not "pure".
What made the previous 2 games good was making the plot having THE LEAST assumptions about the main characters motivations and the choices when presented always being logical or coming from logical reasoning.
And yes, previous 2 games are more "epic" in the sense you single handed saved the world, either from being dipped on FEV and doom mankind (Super Mutants are sterile) or rest of the world (and that includes YOU) being killed by a virus.