Firstly this was not written by me. It was written by /u/JE_SAWYER_IS_MY_HERO (Possibly the best commentator on /r/fallout) and all credit goes to him.

The orriginal version with proper formatting can be found here: http://pastebin.com/AUdw95BT

1. The entire setting is messed up. Fallout 3 seems unsure of when it was supposed to take place. The official year is 2277, but people are still foraging for food. Water is somehow still irradiated. Then there's the Megaton-Vargas issue. Little Lamplight. There is quite a bit of evidence that suggests that Fallout 3 was supposed to take place around the same time as Fallout 1, but that Bethesda wanted to shoehorn the BoS, the Enclave and Harold into their game to try to appeal to older fans so they change the year.

2. Unexplained lack of damage. For some reason, Washington, DC appears to have comparatively very little damage to it, even though it is the capital city of the US, and the home to the White House and the Pentagon. Following established lore, every bomb used in the Great War would have been between about 450kT and 800kT. We see that the White House was directly hit with a nuke. If a 500kT bomb hit the White House, almost the entire Mall should have been pulverized... and yet we see the Washington Monument standing.

3. Mothership Zeta's* very existence. For one thing, they legitimately decided to claim aliens are canon. If you've followed Fallout lore, you'll know that one of the central themes is that humanity is the bringer of its own doom. It's made very clear that the Great War was caused by humans. In Mothership Zeta, there are documents that tell you aliens had access to nuclear launch codes, and it is suggested that the aliens launched the first bombs. This almost entirely attempts to deconstruct Fallout at its very core.

4. Vault 87. If you know the lore, you know that FEV does not do what we see in Fallout 3. Super Mutants do not become towering, retarded giants as they age. There is an explanation offered in the game, but this explanation does not make sense, further denying credibility to Bethesda's writing. This is another example of Bethesda sacrificing lore accuracy, rationality and story for "visual bling" - they wanted towering mutant giants, so they completely fucked up the lore behind FEV to accomplish this.

5. Expanding on point #1: Lack of progress. Following the lore, everyone on the West Coast is already settling in. It's been 200 years after the war. At the time of Fallout 3, the NCR would be pushing one million citizens. They have public transportation, wage jobs, a domestic army, working cars/flight for the super-upper class, bureaucracy up the ass, voting, government, agriculture, mining, construction.. the world is already moving on. Yet, in Fallout 3, people still live in shacks and scavenge food from the local Super Duper Mart? Makes sense.

Minor grievances:

1. Nuclear weapons are not treated as seriously. In Fallout 1 and 2, there are only two nuclear weapons (one per game) that are ever shown... and they are portrayed as being so incredibly serious and fearsome that even the bad guys are reluctant to use them. In Fallout 3, you can blow up an entire settlement within the first ~5 minutes of leaving Vault 101, and after another ~15 minutes you can get to GNR where they give you a weapon that fires "mini nukes".

2. Lyons' Brotherhood. In Fallout 3, the two Brotherhood factions are mislabeled. Lyons' Brotherhood are the real outcasts, and the Brotherhood Outcasts are the real Brotherhood of Steel.

3. Lack of moral ambiguity. Another of the recurring themes of the Fallout series is the idea that there is no absolute morality. At many points in the games (except Fallout 3) you have to make a decision where no matter what you choose, there will repercussions. The easiest demonstration of this would be in Fallout: New Vegas. The side you choose to support for the Second Battle of Hoover Dam decides the fate of the Mojave, but every single choice has its pros and cons.

4. Poor storytelling. None of your decisions have any impact, save for the very last one. The characters are all one-dimensional and bland. The plot is cliched and uninteresting. This is just "another nail in the coffin" - by itself it might not have been a big deal.

5. Megaton. Why in the fuck would people build a settlement around an undetonated nuclear bomb when Springville is practically down the road, and largely intact. Not to mention, why is the crater that big? It's an unpowered gravity bomb, for crying out loud.

EDIT: Gosh people, don't kneejerk downvote please.