I've seen a lot of suggestions for Settlers Of Catan for 2 players. Some are even officially endorsed. All of them have a problem with trading. Some require special attention to set-up, like playing with a smaller island. Others have too much space that two rivals never manage to get in each other's way. A few try to solve that by having both sides play with twice as many pieces and double the victory condition. Some just modify the rules so much, like rolling twice per player's turn, that it just doesn't seem like Settlers Of Catan anymore.
The ideal solution also seems to me the most obvious. This variant should allow plenty of trading, requires no special set-up, reflects the full game's spacial limitations, and keeps most of the rules the same. Best of all, it still feels like Settlers Of Catan.
So I present to you ...
The Two Settlers Of Catan
Both players select two colours to play. To begin, determine who will go first. The first player chooses one colour to be first (blue) and which is third (white). The second player chooses one of her colours to be second (red) and which is last (orange).
Now play like normal.
1: A player must keep resources for both colours separate. When not in use, resource cards should be kept face-down next to unused pieces of that colour. Both sets of cards should not be handled at once.
You can examine your other colour's resource cards at any time. It would only bog the game down while players try to memorize their alternate cards before starting their turn and this isn't a game of memory.
2: A player may only make trades with one of the opponent's colours at a time. While multiple trades can occur on any turn, a player cannot trade a resource to one of the opponent's colours and receive a resource from the other.
Example: Blue cannot trade a resource to red and receive one from orange in return. Blue can swap resources with red and then swap resources with orange Blue cannot trade, give, or take any resources from white.
Clarification: The robber acts as normal and players can steal from their alternate colour. If such a thing occurs, the opponent may opt to shuffle the resource cards among the pile to be stolen from.
Optional: If it helps, use turn markers to keep track of the order by placing a 1, 2, 3, and 4 in front of the unused pieces of corresponding colours. You can also have a token to pass around to place by the active colour pile or you can just keep the dice there.
Optional: You might also wish to say that to win, one player's colours needs at least 10 points while that player's alternate has at least 5 points if you are concerned that someone will try to have one colour throw the game in favour of the other, but you'll probably find that this isn't to said player's benefit anyways.
So that's it. Two simple rules. Appropriate number, I say, for two players. No changing number of dice rolled, cards held, tiles used, victory points needed, or collective number of pieces used.
You can think of this as a four-player game without missing a beat. Although this variant does prevent trades between the "opponent across from you" there are plenty of times in Settlers Of Catan where a player will simply refuse a trade of seemingly mutual benefit.
Your "opponents to your left and right" may still wish to trade because furthering your progress with one colour still does nothing for your other. Also, the only way to get a resource to your alternate colour is to trade it to your opponent first and hope you can trade for it next. There's a price to that, of course, as it would otherwise be a very powerful move.
You can play 2-player Cities & Knights and Seafarers with this variant. I've never played any of the other alternatives, but from what I know of the volcano and fishermen, this shouldn't cause any problems there. If you try it, let me know what you think!
This is pretty much exactly how my fiancée and I normally play Settlers against each other. Like you, we've kept the option up our sleeve to require a minimum score for your second-place team, but haven't needed to use it. The inability to trade between your own two colours seems to work well enough to prevent players using one colour helping feed the other, even though robber and settlement placement can still be used to 'collaborate' between your two colours.
The biggest problem we have is keeping track of turn order so I would recommend your suggestion about marking the turn order. A bigger potential problem is forgetting which hand is which - but the reason that sometimes crops us for us is that we tend to play in less-than-ideal places, e.g. the couch (we have the travel edition). On a table with enough room to lay out cards and pieces properly it shouldn't be an issue...
Rather than getting one to 10 points, how about getting both to 8? That would enforce the 'split time between two' meaning that both would really need to trade with the opponent to keep going?