The delta between outside air and air in the combustion chamber will form condensate that will drip onto the burners and floor pan. The walls often get it too. This phenomenon is why furnaces and boilers have double walled flue pipes. Pool heaters, even with a high wind stack, don't have this.
As was mentioned before, there are heaters that have higher efficiency ratings but are substantially more money. The materials used are more costly.
One thing no one has mentioned, but that I was allowing for was the potential for a heat pump. But how the OP answers the questions I raised would suggest whether that was a reasonable solution for his needs.
Scott