Yes manual transmission is better in terms on maintenance / fuel efficiency / control
I don’t think these days manual cars has good resale value
Depend on your driving habit and kind of drives you take.
There are now tiptronic gears for people who want to have a minor manual control over automatic gears, but for tiptronic the gear system is automatic itself but with limited manual override features, just to give the driver the manual gear pleasure. The problems of maintenance and fuel economy of automatic remain the same.