Instead of a consistent and logical world, we get "cool shit". What's cool shit, you ask? An excellent question. Cool shit is whatever stuff random Bethesda designers thought would be cool. To be honest, Fallout 2 was also sporadically guilty of this syndrome, but Fallout 3 takes it to a thoroughly different level.
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Overall, it would be easy to write a report worthy of an EU bureaucrat listing all the silly and stupid things Bethesda has shoehorned into Fallout 3. The biggest problem is not so much that it isn’t Fallout, but rather that the setting doesn’t make any sense whatsoever. Bethesda had an opportunity to craft a cohesive “living & breathing” world, but instead chose to build an amusement park with a bit of everything ‘cool’ they could think of. To be fair, some things Bethesda did are brilliant and atmospheric, but they are isolated elements that never form a coherent and consistent world that makes even the most basic sense.
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"Violence done well is fucking hilarious."
Todd Howard, a boy-genius
Unfortunately, the combat system is mediocre at best and the only thing that could be described as "fucking hilarious" is Bethesda's failure to come up with something interesting and engaging.
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The main quest is one of the game's biggest weaknesses. It doesn't make sense. The water contains radiation and thus isn't safe to drink. Maybe if people stopped playing with nuclear catapults and blowing up nuclear cars, the situation would improve… Anyway, even though it's relatively easy to purify radioactive water - see the quote above - top East Coast scientists, including your dad, have been trying to find a much more complex and unnecessary solution, known as Project Purity. They fail miserably at first, then you dad enters that "shall never be opened" Vault 101, raises you, but after watching a Blues Brothers rerun, decides to put the band together again and leaves the vault. You have no choice but to follow him, so the "shall never be opened" vault is opened again.
You spend some time searching for your father, asking everyone "have you seen my father, the middle-aged guy?", and that's the best part of the main quest and the game. Once you're reunited, the game hops on rails and takes you on a magical tour through one of the most idiotic game endings in the history of video games. Investing into a pair of good writers and story-tellers should be the top priority for Bethesda. The drop in quality, comparing the game to Daggerfall and Morrowind, is very noticeable and painful to experience.