Vault 87 was also a special vault in that it was in reality not a vault at all rather an underground science base used to experiment with FEV. Vault 87 was very odd to me because of its exclusive use as a FEV laboratory, I thought the official canon had established the military, not private contractors like Vault-Tec, had taken FEV off the market sort of speak.
The initial work was done by a private company, West-Tek, at the request of the military. When it began showing promise as a means of creating super-soldiers, the Army slammed a lid on the whole deal and moved it to Mariposa Military Base. At no point was Vault-Tec involved in the research, which is why the concept was such a huge controversy when FO: Brotherhood of Steel came out with its "Secret Vault."
As to the robot, it was out of desperation as were the G.E.C.Ks that were considered experimental by Braun, however, in Fallout 2 there is apparently two G.E.C.Ks per vault.
But see, that's it, G.E.C.K.s were never considered experimental. Considering that they're the vault equivalent of a road-side emergency kit, they would be fairly simple to produce compared to something on the scale of Liberty Prime. Really, the only obstacle to getting Liberty Prime running was power production and management, something that would have benefited from the resources that were instead funneled into mass-producing a briefcase-sized Genesis Device.
G.E.C.Ks aren't the end all be all in technological progress, though, as I am to understand, rather they contain some seeds for planting, chemicals to bring life to bad land and information on how to build a city.
Which is exactly what they were meant to be as detailed in FO2. But suddenly in FO3, they've become capable of breaking down everything with a certain radius and reorganizing the matter into green and lush paradise. It says as much if you attempt to activate the G.E.C.K. while retrieving it from Vault 87. That is technologically far more advanced than anything that 2077 America should have been capable of producing. I might believe that Braun was enough of a genius to produce a functional example, but certainly not in a form that could be mass-produced. And it would be the height of stupidity to place that in a vault that has a high chance of failure, rather than in one of the control vaults that are designed to work exactly as intended.
With how many of the vaults that failed around DC it becomes possible that because of some of the experiments that went on in the vaults, or their very nature, G.E.C.Ks weren't sent to them. With how many were being "disposed" in Vault 87 it becomes very plausible that Vault-Tec believed they would only need one for the research team that should have been left, just because G.E.C.Ks were standard issue in most vaults doesn't mean every vault. Were talking about corporation here, not the Soviet Union.
I'm willing to believe that the lines about every vault being issued one were based upon a case of false advertising, namely that Vault-Tec knew people would not sign on the dotted line if they were told that their vault might fail, so they created the illusion that every vault had the means to rebuild itself once the timer wound down. For example, it makes no sense that vaults like Vault 101 would have a G.E.C.K., as it was never intended to be opened, or Braun's little fantasy land in Vault 112. And you could stretch it a bit and say that Vault-Tec knew some vaults were destined to fail and didn't want to waste the money in providing them a G.E.C.K. Of the vaults in the Wasteland, the easiest to believe would fail might be Vault 108, where it was designed to be handicapped pretty much from the start. But Vaults 87, 92, and 106 all seem to have the same story, namely that the experiments started going off without a hitch, and then a small error caused things to get out of control. Why would Vault 87 get a G.E.C.K., but not Vault 92 or 106?