Mothership Zeta was a great DLC but I know plenty of people who were upset about the Zetans presence due to the silliness involved. The Zetans are, of course, part of the UFO craze in the 1950s just like Scientology was born from similar values and thus makes sense to include the Hubologists (albeit--Fallout 2 didn't seem to be interested in the actual weirdness of Scientology and the 1950s--they just wanted to make some cheap Tom Cruise jokes).

On my end, I like the Zetans but I'd actually prefer it if the Mothership Zeta campaign remained canon but got retconned a bit. There's all manner of weird science experiments and oddball false flag operations in the Fallout universe so you could easily give another origin for the Zetans than they're actually aliens.

You could easily do the Institute as behind them, for example, with the Zetans being a cover for the organization's kidnapping of people across the Wasteland. The various "out of time" people you meet on the ship could all turn out to be Synths and not know it. Obviously, this would only be in a terminal somewhere to read about but might be fun for something to find in a DLC or something similar.

A pity that we didn't visit Area 51 in New Vegas as that could have been overrun with Zetans.

Hehe.