2. The first title to get a question gets precedence
If people start asking questions about Godzilla (1998) first, then that title gets the original tag, godzilla, and the original would have to live with godzilla-1954 if and when people want to ask questions about it.
After thinking this over for a while, I think 'Popularity' and 'First come first server' are probably the same thing: chances are people will ask about the most popular title first, and I think that version should be the one to get the original tag.