Setup Sections:
I think the Basic Setup and Special Setup sections can be combined, integrating rules from the expansions better by having the subsections not be the expansions, but the type of setup required. I think this would make it a lot more readable and be more consistent with the rest of the document.
For example, you could do something like this:
Setup
The Supply
The cards in the supply are the cards available to be bought. Place the supply piles face-up on the table, as follows.
The Kingdom: 10 piles of different Kingdom cards. They may be selected in any way you choose. Each pile of Kingdom Victory cards should include 12 copies of the card. For two player games, include only 8 copies of Victory cards. All other kingdom card piles has 10 copies of the card, unless noted otherwise below in [the section] Additional Setup.
Basic Treasure card piles: Copper (60 cards minus the starting Coppers for each player), Silver (40 cards), and Gold (30 cards). If playing with 5 or 6 players, use twice as many Coppers, Silvers, and Golds.
Basic Victory card piles: Estate, Duchy, and Province. Include 12 copies of each. If playing with two players, include 8 copies of each. If playing with 5 players, use 15 Provinces, instead. If playing with 6 players, use 18 Provinces, instead.
Curses: 10 cards in a 2-player game. Add another 10 to the pile for each additional player.
Determine whether to include Platinums and Colonies randomly based on the proportion of cards from Prosperity in the kingdom.
Small text note: One way to choose randomly based on the proportion of kingdom cards from a named expansion is to take the randomizer cards for the cards in the kingdom, shuffle them, and then draw one card. If the chosen card is from the named expansion, the draw is a success; otherwise, it is a failure.
If any card in the Kingdom has [P] in its cost, include the 16 Potion cards in the supply.
If any card in the Kingdom has the type Looter, include the Ruins pile in the supply. Shuffle the 50 Ruins cards, and from those draw and include the same number of Ruins as Curses.
Additional Setup
If you are using Events, include some randomly. No more than two are recommended. Place the Event cards on the table separately.
[[Describe by card, alphabetically, special set-up rules such as the number of cards, tokens, mats, non-supply piles to include, etc.]]
Trash
Place the Trash card on the table to indicate the trash pile (or "the trash").
Starting Deck
Each player begins the game with a deck of 10 cards: 7 Coppers and either 3 Estates or 3 Shelters. Determine whether to play with Shelters randomly, based on the proportion of cards from Dark Ages in the supply. The three Shelters are Hovel, Necropolis, and Overgrown Estate.
Starting Hand
Each player draws 5 cards from his deck to form his starting hand.
Choosing the Starting Player
Randomly choose the starting player. When playing several games, the starting player is the player to the left of the winner of the last game. If there was a tie in the previous game, randomly choose the starting player from the players that didn't win.
Turn Order
Players take turns in clockwise order.
Edit: Typo.