I said that aside from those things, there is not much difference. The only obvious unavoidable "supernatural phenonmenon" is the flashback, and to me the degree to which that is truly supernatural is debatable.
Besides, this is not the first time that Fallout has had some "ghostly" phenonmenon associated with it (Fallout 2 with an actual ghost, Anna Winslow).
I would disagree on this, I find the Obelisk to be hidden well-enough to be considered an easter egg. I completely missed it the first time I went through dunwich myself. If the Obelisk was sat smack dab in the center of the building with all the ghouls worshipping around it, then yes, it would be too obvious for me.
Again, I have to disagree. I thought Dunwich fit the wasteland setting well enough. Aside from the supernatural elements, it also has a very atmospheric backstory concerning its orginal function as a office building which denotes its post-apocalyptic setting. You apparently feel differently, but I suppose thats the difference between someone who likes Fallout 3 and dislikes it. However I would like you to recognize that saying "it doesn't fit the game at all" is a matter of opinon, one mans trash is another man's treasure so to speak.
A bleak wasteland that is reminisicent of the idea of "paradise lost" is exactly what characterizes the game for me. I'm afraid that all that "goofy content" did not stand out to me. It may bother you to no end, but I have never found a game in which I was moved by the setting as much as Fallout 3. Take that as you will.
Fallout 2 also had many "goofy inconsistent aspects" as well.
Edit: Also just for the record, Okie and Sitruc, the arguments you are presenting have been brought up multiple times before, with no clear resolution. Its a matter of preference in my opinion, if you like Fallout 3 and think it has a good place in the Fallout series, great, if you don't, then thats fine too. I've found that there is no chance of changing the others mind if they are a steadfast supporter of one side of the other, so I think it would be best to just holster your guns and walk away.