I pretty much always play with a manual transmission now. I only use Auto if I'm just screwing around, but with manual I know I've got a lot more control and can eek a little bit more from the car I'm using.
Automatic for the first time playing the game so I can get adjusted to the steering and the control of the game. Once I am adjusted and accustomed to the game style, I could play manual if I wish to do so.
Is there any difference between Manual and Automatic? Control wise of course there are, but I mean in terms of speed and physics? I always wanted to try Manual but didn't know if there are benefits, so I stuck with Automatic.
Being a fan of hardcore simulation, I can tell you that manual is way better. Having full control over your car is much better than some stupid AI automatically doing it and screwing up in the process. It's impossible to drift with an automatic gear, and that's one of the essentials of the rally games I love playing.
