Well you are forgetting the clearly alien corpse that the Shi had before being stolen by the Hubologists; your probably going to say that it wasn't confirmed as an alien body but I would say that that's willful speculation. Besides, the WW trait does non-canonise the events.
I would not have minded them in FO3/NV if they were already dead, and that was all there was to it.
The problem is one of assumption and of design. In Fallout you could never visit the alien crash twice; theoretically, you could never mention it or bring anyone else out there to see it. Anything in the wasteland ~ was just weird; until FO2... Then you get the scorpion chessmaster, the Brain and a live King Aurthur (which could be just loonies; IIRC the rabbit and hand grenade were not available without cheating).
The DLC was a mistake, the encounter was not.
And skydiving whales, lets not forget that.
Edit:
We all know the origin of the http://www.youtube.com/watch?v=tpiwRN6OA2A right?