added in more to appeal to the typical board game players (which, to be fair, is probably the anticipated audience) than strongly incorporated into the mechanics themselves.
No, some people like to think that RGG made a marketing-based decision on the flavor, but really, I didn't have any medieval-themed games at the time, had been meaning to do a kingdom-building game, and thought this was a reasonable fit. In the main set, Circus was renamed to Festival, Militia and Bureaucrat switched at one point (see Secret History), and everything else has the original playtest name.
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Dominion is a simple game. That means the game isn't adding rules just for the flavor. The cards themselves do support flavor to varying degrees, but the best flavor requires the most text. Thief was easy, but nothing was ever going to be great flavor for "+3 Cards."
At the micro level, there are the cards. There are some themes that are obvious/easy to perceive (villages being the obvious...but then there's University and Festival). Here are some cards that I just don't get:
The idea is that +2 Actions is a group of people doing things for you. Most of them are Villages, but this is how University and Nobles fit in.
Baron: Nobles is a victory card; Duke is a victory card; why not Baron?
It's not like that. Why aren't Nobles and Duke tracts of land, that's the question. And the answer is, well Duke is named that because it involves Duchies, and Nobles uh well maybe they're attracted by the tracts.
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Baron involves Estates, that's how it got that name. He's a real Estate Baron.
Library: Library lets you set aside action cards, which often leaves you with a handful of victory cards and coins. Why does a library get you those? Shouldn't it get you actions? My guess with this particular card is that it originally did get you only actions, but was probably overpowered in that version.
No, it didn't change except for the precise wording. Library was the kind of name I wanted in Alchemy, where the card started, and well I guess I've been influenced all these years by MtG equating card-drawing with knowledge. There is no such equating in Dominion; I decided early on that "+Cards" would have no flavor, because a card like Torturer wants to be named for the relevant new part of the card, not for the +3 Cards.
Chapel: What does trashing cards have to do with chapels? Is there a theme with religious figures/buildings/rooms and trashing (e.g., bishop)? Why?
Well this one is easy. When you trash Coppers and Estates, you're giving them to charity, and when you trash Curses, that's an exorcism.
Those a few off the top of my head, but I know there are others that come up (are all attacks themed as people? What is the mechanical difference between a card representing a person and one representing a building? Why only use verbs on the trash for a new card effects (remodel, upgrade, etc.)
There's no specific reason for person vs. building, just whichever sounds better on the card, except yes, attacks are usually people. Remodel was a verb and then the rest just imitated it. One-shots were events, back when there were more of them.
moat's defensive ability fits its flavor perfectly, but why does it draw cards?
Because it would be too awful if it didn't! And really that sums it up. You are not gonna do better on naming Moat; you really have to just ignore the +2 Cards when naming, except when that's all the card does. And then, do you drop the +2 Cards so the card has better flavor? No, you do not do that, it doesn't matter how good the flavor is on a card no-one is ever buying.