Cards can be ranked in a variety of ways. You can rank the villages. If you do so, you just have to consider cost as part of the overall goodness of the card. Like, Bazaar is a real good village-type card, but it's a bit pricey. So it ends up in the mid-to-upper tier on the village rankings.
You can rank the cards based on cost (as we do here). If you do that, you are taking into account the other elements of the card when you rank it. Think of, whatever way you set up the ranking, that thing is the thing you are holding constant. When we ask "What are the best $3 cards?" we are saying, let's disregard cost, look at all these things with the same base cost, and compare them. Lookout is fine, it does some nice trashing and sifting and it's non terminal, but sometimes you hit good stuff and it doesn't replace itself so it's kind of meh. Doctor is terminal, which is not so good, but hey, it's trashing is stronger in the early game and also you can overpay for it and do this cool thing. The overpay aspect is just an aspect of the card we are looking at here as we hold cost constant.
Or else, I demand a Duchess category. It's the only card that's price is "You bought a Duchy." It's the best card with the price "You bought a Duchy"!