I much prefer manual transmission, you have much more control over the car
Do you? How?
I have a manual licence but drive an automatic. DH has a manual licence but his dad gave him his old car when he passed his test (which was an automatic) so DH has always driven an automatic.
I would agree that a manual car is less limiting with hire cars and the like but given that people can't wind down a window, put their own lights or windscreen wipers on, or read a map, I can't see that letting the car do the gears for you is a particular problem. One of our cars can be driven in manual mode so I effectively drive it as a clutchless manual.
I have no idea why we are so wedded to manual cars but people will drive automatics as hybrids and electric cars become more commonplace. I'd say do whatever suits you.
As for hire cars, you just need to book in advance. I don't often need a courtesy car but when I have I've been able to get an automatic on all but one occasion.
if something goes wrong with with the gear box, autos are more expensive to fix and generally more expensive to purchase
do things go wrong with the gear box? We've driven automatics for 20 years and never had to replace a gearbox. Other things have gone wrong, but the gear boxes have been fine. The one thing I would say is that you may well go through tyres more quickly but I don't say that with any scientific authority, just a feeling.