Regarding that egregious definition of plot-holes by the OP/troll, this is the actual definition
An inconsistency in the narrative or character development of a book, film, television programme, etc.
https://en.oxforddictionaries.com/definition/plot_hole
From that definition, I'd argue that Fallout 3 just happens to be a giant plot-hole in the story of the Fallout franchise after 2 onwards. Plenty of inconsistencies with the overall idea of the series (among other things) and the explanations used to justify the inconsistencies are rather poor.
Credit to
@Risewild for the list below on 3's lore inconsistencies:
Major Stuff:
The G.E.C.K.
Bethesda changed a few things about the G.E.C.K, which directly affects Fallout 2 lore:
Fallout 2 directly states that the standard issued equipment for every Vault was 2 G.E.C.K. units, but in the Capital Wasteland there is only 1 G.E.C.K. while there are 6 Vaults and no signs or justification to what happened to the other G.E.C.K.s.
There is also a terminal with an official Vault Tec message saying how lucky Vault 87 was for getting 1 G.E.C.K.
Bethesda also turned the G.E.C.K. into a magic matter disassembler/assembler:
Fallout 3 Loading Screen said:
The G.E.C.K. will collapse all matter within its given radius and recombine it to form a living, breathing, fertile virgin landscape and allow life to begin anew.
While in Fallout 2 it was just a bunch of stuff in a suitcase. It had:
- A cold fusion power source
- A bunch of seeds
- Some soil supplements
- Some chemical fertilizer
- An encyclopedia containing lots of useful survival, building, farming, etc. information
- Some codes for allowing the Vault replicators to make a few stuff like special clothes
- A pen flashlight
This is a really big lore break, since the G.E.C.K. is an essential part of Fallout universe lore and the second Fallout game revolves around this item for it's main quest for most of the game.
Nuclear Vehicles
Fallout 3 depicts all the vehicles as being nuclear powered, which is a big retcon from previous Fallout games, where there was no nuclear vehicles at all. As a matter of fact, the Great War was because of the last oil deposit. If all the vehicles (including cars, trucks and motorcycles) would have been nuclear powered, there wouldn't have been the need for a war to get the last oil deposits.
Another thing that this contradicts is that it was stated that the USA had grounded all of their air vehicles because of not having enough fuel for them. That was why the Vertibird was being developed.
Also the reason to create the Power Armors was so soldiers could carry heavy artillery and supplies without the need for trucks, tanks, etc. which consumed oil based fuel.
But if all the civilian vehicles were nuclear powered, why weren't the military vehicles also nuclear powered?
Ghouls
Bethesda changed ghouls so much that they should be considered a different ghoul type (just like they did with the East Coast Super Mutants):
- Ghouls mutation would take a long time in Fallout lore, then in Fallout 3 it could be instant (Moira Brown)
- Ghouls physiology totally changed in Fallout 3, when compared with previous Fallout games. In the previous lore, ghouls were slow and decrepit mutated humans, they couldn't run and had to move carefully and slowly because they were prone to injuries and broken bones.
- Ghouls were immune, but not healed by radiation in previous Fallout games. Not only was the whole "ghouls are healed by radiation" never mentioned in the classic games, but both Lenny (which is a professional doctor) and Gordon talk about how they need Vault City's medical technology to heal themselves (Gordon even says that without medical technology, they will all be dead in 20 years). Why would they need medical technology to heal themselves (if radiation healed them) while they live in a radiation-leaking nuclear power plant?
- Ghouls wouldn't become "feral" animal-like creatures. They would get crazy, but still behave like humans. They would attack strangers on sight, using any weapons they had with them (including guns) and not like an animal
- Glowing ones didn't release radiation from their own body and didn't have the ability to create bursts of harmful/damaging radiation as a means of defense
F.E.V. Timeline
Vault 87 timeline doesn't match with the previous lore F.E.V. related timeline.
Vault 87 construction was started on 2066 and finished in 2071, each vault was constructed for a particular objective, and Vault 87 objective was to work on the
Pan-Immunity Virion Project in conjunction with Mariposa. But the
Pan-Immunity Virion Project was only formed in 2073. So how did they managed to make a vault that had the objective of working on something that was only thought about 8 years after the vault started it's construction and 2 years after the vault was finished?
Stuff with varied importance depending on the person thinking about it and/or how you look at it:
- Creature and robot designs
- For some reason robobrains now have built-in weapons and can't use normal guns
- Mr Handy robots now float using jet propulsion (instead of the fans/propellers), have a blade-saw and a flamethrower for some reason and only have three arms/tentacles
- Eye bots were changed from an hovering sentry equipped with an electric prod, into a round hovering radio with a laser weapon
- Molerats are very different from the ones in the previous games, and they resemble way more the pig rat creature from the classic games than the mole rats
- Etc.
- Jet being so abundant and also being found in pre-war containers in the East Coast
- Power Armor now requires specialized training to be equipped
- Vault Door's design. This new design of opening into the vault would make the doors resist less force than the classic games' doors that open out of the vault
- There is no reason at all for caps being used as currency in Fallout 3. Caps are used in Fallout 1 as currency because they are backed by the powerful Water Merchants
- There is no reason for Centaurs to exist in Fallout 3. Centaurs were an experiment using animals and humans merged by FEV. East Coast Super Mutants couldn't pull something that complicated. Not to mention that the Centaurs in Fallout 3 seem to be all human parts. Since you can't "control dip" several humans at once using Fallout 3 FEV (it's airborne, not liquid), there isn't a convincing way of making a centaur in Fallout 3
- Radiation sickness affects humans in different ways in Fallout 3
- Fallout 2 lore says that the Enclave was destroyed in it's final credits, but in Fallout 3 they are going strong (possibly even stronger than in Fallout 2). Their numbers are impossible to achieve with the explanation provided in Fallout 3 (that the East Coast Enclave was formed by some Enclave remnants that traveled the country when contacted by Eden after the destruction of the West Coast Enclave) when compared with the lore of Fallout 2 (where the Enclave was dead and only a few survivors were left)
- Elder Lyons' group main mission was to contact the Midwest Brotherhood of Steel in Chicago, but they said they couldn't find the Midwest BoS. This is quite a retcon because the Midwest BoS controlled a massive amount of territory (as large as the territory controlled by Caesar's Legion). It would be pretty impossible to not be able to find them
- How the Brotherhood of Steel kept sending reinforcements and supplies from the West Coast to the East Coast until they found out that Elder Lyons was disobeying direct orders is also lore breaking. The West Coast BoS was tiny by the end of Fallout 2, they were always small because they didn't really recruited more people. Fallout 2 shows and tells us how weak and understaffed the BoS is. There would not be enough troops or supplies to keep sending through the entire country over and over
Small and tiny Stuff:
- Tesla Armor was a fancy Metal Armor, not a Power Armor.
- Weapon changes:
- Like the Power Fist and Super Sledge, which changes how the weapons would work
- Rocket Launcher changed into Missile Launcher
- The 9mm Mauser (a german weapon) was turned into a Shanxi Type 17 (chinese weapon) but instead of using 9mm ammo (like the Mauser) or .45 ammo (like the real world Shanxi Type 17), it uses 10mm
- 10mm Pistol changed from the Colt 6520 10mm autoloading pistol into the N99 10mm pistol
- Assault Rifles went from using 5mm to 5.56mm
- Hunting Rifles went from using .223 to .32
- Pulse, Laser and Plasma weaponry design (including grenades)
- Etc.
- Nuka Cola is now radioactive and lost it's addictiveness
- Stealthboy technology works differently now
- All "personal" computers are several times smaller and have their own power source now
- Radaway works differently and lost it's addictiveness
- Vertibird design is quite different
