Auto is better with resale, in terms of fuel consumtion...manual is a little better but not much. Maintainance - its not hard at all, especially with the new Auto Trannys these days - You'd have to work real hard to kill a modern-day transmission, especially if its an imported car we're talking about.
People tend to think manual is a lot more fun than Auto to drive - but it depends. Personally, I prefer Auto these days - but when I was 16 - I preferred a manual