Even New Vegas has its own inconsistencies with lore established by prevous games. Here's one I've found - Mr. Handy is identified in the REPCONN museum as a RobCo robot, even though it was previously established as a product of General Atomics International.
Should I find any more like the one Ausir mentioned I'll post it here. Busy with my second walkthrough.
Elder Maxson in the first game personally gives you the mission to go to the Mariposa Military Base and stop the supermutant production facility. Yet in New Vegas, the Courier learns of the "Chains that Bind" which clearly state that an elder cannot give out orders to anyone who is several deviations of rank lower than themselves. Paladin Mathia seems totally fine with this going on right beside him, too. Conclusion: The "Chains that Bind", though a clever plot device, has no precedent.
Perhaps - but even in Fallout: Tactics (I know, semi-canon), the Brotherhood of Steel issued orders directly between General and the main character. I think the "Chains that Bind" was a little short-sighted, to be honest, if not inconsistent with the lore. I took a look at the Brotherhood information at the Hidden Valley bunker just now. Dates are not explicitly expressed, but it states that the chains that bind are: "The Chain That Binds is the cornerstone of our organization, the rock that supports the great tree of the Brotherhood and its myriad branches."
It's probably just an outdated and half-forgotten rule no one takes seriously, because(practically speaking) it's kind of silly.
The chain that binds, actually means that the elder can't issue orders to people who are under direct responsibility of another, such as a head paladin or a head scribe. Therefore Elder Maxson can issue order directly to the vault dweller because he isn't the under the responsibility of any head paladins or head scribes, or any other kind of higher rank.
So in the cases where an outsider becomes an initiate he can jump the chain of command? Interesting. I never knew that piece of conjecture.
The Vault Dweller was never assigned under the direct command of anyone else, so Maxson was not breaking the chain of command.
Cabbot from the Lost Hills bunker also receives orders from the Maxson, and not Vree, as would be appropriate under the auspices of the Chain that Binds.
The issue is with issuing them orders without the knowledge of their direct superiors, I think. I doubt Maxson issued any orders to Cabbot and hid them from others.
Section 2 of the Chain that Binds states explicitly: "Orders are to observe the flow and not skip ranks. A superior may only give orders to his direct subordinates, and not to those beneath him. In this way harmony of intent and cohesion of thought is maintained."
This makes the most sense to me if we're going to reconcile the inconsistency. It'd be extremely hard to enforce on a day to day basis, much less a military operation, so I can see liberal exceptions being made. It's pretty clear that when invoking the Chain That Binds to depose McNamara, you're abusing a petty technicality that nobody actually cares about.
Elder: Hey there Initiate whatwasyourname, bring me a coffee! Initiate: No can do, Sir, the Chain That Binds does not allow me taking your direct orders.
Man, I was thinking the exact same thing. "Sir! You asking me for coffee means you are no longer fit to lead!"
If canon is FO1 -> FO2 -> FONV, then I don't really see any glaring errors. If canon is FO1 -> FO2 -> FOT -> FO3 -> FONV, then the BoS is one big jumble of wrong.
Canon is Fallout 3 took place in an alternate universe where everyone's Intelligence score was actually -57 and thus everything wrong about the game could be attributed to gross mental retardation amongst the entire populace.