allow two players when it's a game between friends.
I play Seafarers with my friend one on one all the time and we like it that way. Why can't you allow a game among two friends to be played with only two people?
The official rules only allow playing with 3+ players. The game is not balanced to be played with 2 players. Trading does not work very well, if one player gets ahead, the other one can do nothing to stop him. There is no official version for a 2-player game I think.
The game is not balanced to be played with 2 players. ... There is no official version for a 2-player game I think.
Exactly that. However you can always create a custom game with a friend and one computer player if you don't want other people to join.
I agree with the OP. My wife and I frequently play the physical board game with just us 2. We start with 3 settlements and we generally don't trade, although it is not disallowed. If it is a custom game and it is enjoyed, does it matter if it is not as balanced? We don't enjoy playing against the AI.
If you start going down the home rules path you will have a lot of different house rules to implement. Some of these might work together, some not. I think it is better to stick with the official rules at the moment.
There are official rules for two player games. The official rules for the base game are covered in the booklet of Traders and Barbarians. The rules for cities and knights can be found on catan.de. I cannot currently find the official rules for Seafarers anywhere, but official rules were published on siedeln.de. There are official 2 player rules for all Catan's big box expansions. Since siedeln.de is now down you may have to ask around at the Catan offices for the Seafarers rules, but official rules exist. (I have copied them, but I don't expect anyone to use my copy as an official source.)