I dislike it mainly because I find the figurative use of "vanilla" as "standard" or "generic" annoying. Vanilla is a distinct and unique flavor.
I think for most people (although I do think that vanilla ice cream is generally underrated), whenever they see vanilla and another ice cream flavor on the board, they'll take the other flavor. Vanilla village is vanilla because whenever it's on the same board as another village flavor, you usually prefer the other flavor. However, vanilla ice cream is sort of the standard flavor, so almost any time you would go somewhere that has ice cream, vanilla is an option; hence, vanilla ice cream is easier to get than the other flavors. In the same way, sometimes you only have enough money to buy a vanilla village, and not the fancy $4 village you'd prefer; so vanilla village is easier to get than the other flavors.
Furthermore, as others have pointed out, most (but not all) ice cream has vanilla in it, regardless of whether it is the vanilla flavor. Similarly, most (but not all) villages have "+1 card, +2 actions" (or equivalent) in them. There are still some oddballs, like Native Village and Coconut, but then even that makes sense, because where do you get coconuts? At the Native Village.
I definitely think you're wrong. Vanilla ice cream is the most popular flavor, and there are usually other options. Beyond this, why is it exactly that you assume Vanilla refers to flavors of ice cream? I mean, you wouldn't say 'pepperoni' or even 'cheese' and expect people to know you're referring to something plain, even though those are the most ubiquitous pizza toppings. Or with some kind of frosting or pie or what have you.
I'm not sure I've ever met someone whose favorite ice cream flavor is vanilla. A couple of month ago I remember being somewhere where an ice-breaker question was favorite ice cream flavor, and out of 25-ish, I noticed that no one said vanilla. Vanilla is popular to add to other things (like putting it on pie or cobbler or whatever), but is it really that popular by itself? I don't think I've ever seen someone head straight for the vanilla ice cream at an ice cream shop. My point was that it's one of the most universal flavors - pretty much anyone who likes ice cream likes vanilla ice cream - but most people prefer something else (in my experience). It is entirely possible that my experience is completely off for some reason.
Now that I'm thinking about it some more, I see what you mean. With only Vanilla and Chocolate ice cream available, I could see Vanilla being more popular. Usually you don't have more than two Villages on the board, so I guess the comparison is not perfect.
As for why I assume it refers to ice cream. Most of the time, when I hear the word "vanilla", it's being used
in a Dominion context to refer to ice cream. There are other uses for it, and I certainly hear those, but (again, this is just my experience) ice cream seems to be the most common context, by a substantial margin. When people say pepperoni, I think of pizza, but not when they say cheese (probably because there are so many other common uses of cheese, not so much with pepperoni). If it weren't for that, cheese would probably be even better than vanilla, because I think cheese pizza does all of things I described in my previous post better than vanilla ice cream does. Also, I assumed that the use of the term vanilla in a Dominion context originated from ice cream, because that analogy seemed to fit best (although I'm sure a yogurt analogy works reasonably well too).
And of course you wouldn't expect people to think you were talking about something plain if you call it "pepperoni". Pepperoni isn't plain. Cheese is plain. Pepperoni pizza is cheese pizza with pepperoni on it. That's why cheese pizza costs less than pepperoni pizza. You could call something cheese to mean plain, but there are so many other contexts in which cheese is used that the cheese pizza analogy wouldn't be obvious, so that's probably why it's not commonly used. Pepperoni pizza is strictly better than cheese pizza, because you can just take the pepperoni off, just like how worker's village is strictly better than village, because you don't have to use the +buy. In both cases, that's why the former costs more than the latter. Dude, I think you've sold me on calling it the cheese village.
Edit: Well, eHalcyon's post kind of defeats this one. I guess my personal experience is just way off?