Rio de Janeiro
We divide the settlement, road and city cards evenly between us, leaving the remaining three cards (one of each type) in a small pile. These cards may only be used after all of the cards in a player's personal stack are gone, meaning the one to build the fastest may get an extra settlement.
I fail to see what this accomplishes. You are just needlessly restricting the players's options. And in practice, the only change is that a player now has to build a number of cities before that last settlement.
(Using only the cards found in the base set, there is a chance that the final set of settlement cards cannot be used because all of the region cards are gone.)
You may be playing with some rule wrong. It is impossible to run out of region cards. The expansions change nothing, as they don't add or remove settlements or region cards.
When we play action, unit and building cards, which are then discarded they are put faceup in a single discard pile. When all the cards have been gone through, or we get to a point where we both agree that reshuffling would be beneficial, we reshuffle that stack back into the five draw piles. This keeps the same cards from being rotated and forces us to play with the cards we might not otherwise ever use.
I'm not sure I understand what you mean by "the same cards being rotated". Whenever you discard units or buildings, you place them on the bottom of a stack, and you usually draw from the top. Are you concerned about a player paying resources to search through a stack to retrieve a card that the opponent forced him to discard?
We have made little chits with the dice on them so that we can choose which numbers we want on our starting line-up. It bothers both of us that the starting numbers are always the same.
We have also decided to photocopy each of the region cards so we have two copies of every card, making drawing from the pile more interesting for us.
This may affect the balanced distribution of resources, making some rarer than others and potentially prolonging the game. It also increases the importance of the Scout, which already is a very good card.
We are also planning on making copies of the settlement cards in case we want to play a longer game.
Again, seriously?! The game takes about two hours! Well, to each their own, I guess.