Actually, it makes perfect sense that Vault Tec would have access to the technology of FEV. It makes much less sense that they wouldn't. Vault Tec is a huge company creating some of the most advanced technology in America and they have direct ties to the government, including military tech development. It would be reasonable if they acquired the tech honestly, but it is more probable that they simply acquired it through the time-tested method of industrial espionage.
There is no such thing as an industrial secret and 100% security is a myth.
There are probably other ways to look at Bethesda's development of the lore, but this approach makes perfect sense to me.
As for Bethesda's offerings in Fallout 3, people need to keep in mind that they were rebooting a failed franchise that many of them personally loved even if it was originally a failure from a business viewpoint. They spent millions acquiring the rights to do it. They wanted a franchise that they could develop in alteration with TES installments and the consensus among the team was to try to get Fallout as a good choice for this goal (which they did, of course). In order for a reboot to be a success, they had to compromise somewhat on their stance of developing each game as a "clean slate" because they wanted to attract both fans of the original as well as greatly expand the consumer base with new fans. They had to expand the original lore. Todd originally wanted to simply make a new installment set on the West Coast but Emil and others argued/persuaded him that the East Coast would be a better setting, particularly since it would allow them to develop lore that didn't exist due to the entirely separate location. He eventually saw the value in this approach and now is quite happy with it, at least from everything that we know. Still, they had to include various elements of the original games in some way as an homage as well as a launching point for their vision of the franchise. They did not "break" any lore because they are developing lore in a different location, lore that never existed in the first place.
Fallout 4 will be the first BGS installment where they are truly free to develop Fallout with their own lore, vision, etc. Fallout 3 had a great deal more limitations due to being a reboot, but since it was very successful (and Skyrim after it, of course), Todd now has "freedom to do whatever the hell he wants" as Pete Hines stated in a interview after Skyrim's release. Until we actually have FO4 and play it, we cannot know exactly what vision they have and how the have done in presenting it in-game.
As for the Super Mutants, I think that it is fairly obvious that the Overlords operate as a sort of "Leadership Caste". I also think it is obvious that some of them, particularly the Overlords, have decent intelligence due to the equipment they use (Tri-Beam Laser Rifles, explosives, Assault Rifles, etc.). Their intelligence tends to vary inversely with the evolution of their physical size and strength. Just because their speech sounds "dumb" doesn't mean anything just as it doesn't mean anything for a human. It is their actions and philosophy that "might makes right" and that they are a superior evolution to the non-evolved humans that tends to influence their actions. In other words, we can't really say that certain Super Mutants are literally low intelligence as much as we can say that they are not going to use their intelligence in sophisticated, tactical ways (as opposed to using more of a "brute force" method to achieve their goals). It's more of their choice in reaching their goals rather than an inherent liability they have, at least from what we know.