Noone ever suggested that. What is being suggested that there are some themes that are really not appriorate for Fallout. There seems to be quite a few that feel that aliens is one of those themes, myself being one of them.
Note, this is not an argument of saying whether or not their canon. Although I think it can be argued from in game references that maybe that UFO in the first game was really an experimental air craft stolen by an individual who had been a subject of Mentats experiments (who also, was a big Elvis fan). And clearly, they used an experimental blaster from the same research station that he stole the craft from. However, from the Vault Dewellers perspective, it looked like an alien craft, with an alien pilot, with an alien weapon.
With that logic, suddenly, there are no aliens in game until Fallout 3
Are you kidding? The Pitt is going to be a huge factor in the future of the East Coast in Fallout. Operating a massive steel mill, and actually doing NEW construction rather then sticking things together will have a major impact on the gameworld. It would be a huge disappointment if nothing becomes of that.
As for alien impact on the game setting, if they are overt, it would have a huge impact, unless it's not considered part of the game world continunity.