Checkmate, Finn.
A plain donut or plain bagel are the things without any extras.
A plain cake is rare but is a cake without extra flavors or frosting or whatever. When it just has chocolate even, people still call it a "chocolate cake" and maybe "plain chocolate cake" but rarely or never simply "plain cake". And because the default for cake is to be chocolate, nobody would be crazy enough to say "vanilla cake" to refer to unadorned chocolate cake. So the use of vanilla to mean regular/plain isn't a lost cause! It's worth criticizing to not lose its real meaning.
The pizza analogy really would work like this: say that pepperoni pizza was so common, everyone had that or more complex things and nobody ever had a simple cheese pizza. Then imagine people start using "pepperoni" to mean plain/regular. Metaphorically, they'd start saying "eh, that one night stand — the sex was just pepperoni".
Okay, so, upon reconsideration, it's not "plain" or "regular" or "popular" that vanilla refers to. It's original, as in the first thing that seems default and was around before other stuff. These metaphors are complex.
But I happen to think we should notice when we use metaphors and consider their meaning, question them, use them thoughtfully…
As someone who can't stand the use of "they" as a singular pronoun, I also understand fights against the evolution of language are battles that I won't win.
Please please don't say that. It is not being used to mean that. It is being used in a figurative way to mean "very". This is an ironic but relatively minor shift. It's in no danger of becoming its own opposite.
Vanilla = plain is a metaphor.
Singular they is a syntax issue.
These are processed totally differently in our minds/brains. Both we come to accept with enough usage and good attitude, but they have very different significance in language.
Most people who don't start knowing singular they find it a true syntax error, the sort like a P600 response in an EEG test. It's deeply irksome. But then with familiarity, it goes away.
Metaphors don't have such a deep language processing issue, they just have semantic meaning that we accept or not and our objections live at a far more intellectual level.