Harav Akiva Eisenberg (formerly a lecturer at Aish and Ohr, now retired,) told me something excellent. Our preparation and the order of the meal at the Shabbos table is a re-enactment of Ma'aseh Bereishis.
The order of our preparation and of our meals seems to be inviolate, as if it were set in stone. Who would have a fleishige first course and a main course of fish? Yes, I'm sure it is sometimes done, but it's rare. And as you all know, we put the challah on the table before the candles, ostensibly to prevent a muktzeh problem of Basis L'Davar Ha'Asur, although considering the relative value of the silver candlesticks and the Challah, it's not clear why that would work. But here's what Harav AE told me.
Every step of the process represents the order of the creation of the world.
First Day: Tohu VaVohu, inchoate matter was created to later be properly formed- Preparation for Shabbos. Second Day: Spreading out the Heavens- Spreading the tablecloth. Third Day: Desheh Eisev- Placing the Challah on the table. Fourth Day: The two Me'oros- Putting two candles on the table and later lighting them. Fifth Day: Fish- the first course. Sixth Day: Animals- the main course. Shabbos.
Like many of our symbolic minhagim (such as the Kittel at the Seder, please see my post at http://havolim.blogspot.com/2009/03/fancy-kittels-mixed-messages-and-tides.html regarding the Teshuva in the Igros Moshe in which he says that the meaning of the kittel at the Seder changes depending on the generation and the locale,) the doer's understanding informs the effect of the minhag. Setting the table while saying "In honor of the holy Shabbos" is an entirely different experience than doing it as a tedious obligation. Here, too, while I won't insist that this is the reason for the order of the meal, I do believe that it was a factor in its ubiquity. In any case, it is worth contemplating.