Seems to me that the only vaults that were/are inhabited recently were the ones that had these crazy experiements. I have yet to see in a fallout game a vault that did not have some weird experiement going on. Hm, did the vault the lone wanderor come from have a crazy experiment? I can't remember. (also my "knowledge" is limited to FO3 and FONV, I'm relatively new to the fallout series so if FO and FO2 had "normal" vaults I'm unaware and please correct me.)
Vault 13 was intended to be sealed off for 200 years
Vault 15 had people from variety of different ethnicities and ideologies, NCR is the result. (along with Khans, Jackals and Vipers)
That one vault where everything was supposed to break down all the time.
Then there was a vault which didn't have any entertainmet in it, and its sister vault where they had only tapes of a crappy comedian.
And others.
In designing the vaults which were in NV and 3, Vault-Tec just went full [censored]. For example, plant zombies, white noise, super mutants, psychoactive drugs and Gary clones. Altough, NV had some pretty good vaults, too.