Well I think some of these are over-simplifications (I'm certainly not saying Fallout 1 or 2 had worse storylines) but when you get right down to it, both the Fallout and Elder Scrolls series follow the same basic format, as do many other genre types and games.

-Hero emerges from seclusion somewhere
-Hero orients himself/herself to the world outside (in Fallout 1 and 3 it was the world outside the vault, in Fallout 2 it was the world outside the village, and in Oblivion, New Vegas, and Skyrim it was a world outside of their own past or amnesia).
-Hero is introduced to threat to humanity/world/life.
-Hero works toward overcoming said threat with protagonist faction and in the process shapes the world around him/her and becomes involved in it.
-Hero confronts main faction(s) behind the threat.
-Hero fights main adversary.
-End story.

New Vegas is really the only story which differentiates from this format (in the Fallout series) in that you essentially get to choose who your protagonist and antagonist faction is (a relatively new concept for both series). However it still follows the basic structure.

The details of the story and its coherency is what really makes the story work. Not the overall idea (ie. end of the world saved by hero). Fallout 3 had some trouble with this and the story could have been amazing had these details been addressed.

Fallout 2 and 1 as well as New Vegas did it much better. In my opinion, Oblivion and Skyrim did it fairly well as well.

All Fallout 3 did was lift factions, characters and story tropes directly from the first two games, pepper it with the most inane dialog in video game history and add a nonsensical and ridiculous main quest. Yeah. Totally comparable.

Yeeah, the writing in Fallout 3 was kind of... silly or childish at many times