What are some of the potential problems one could face with an automatic and a manual? (Repairs, parts, costs, maintance, etc....) :)

I suppose the same problems that you can get in any car, it really depends on how you drive one. Doing Neutral drops, can hurt an auto, and powershifting can hurt a standard....unless I am missing your question.

A clutch is cheaper to replace than a 4L60-E.

My Camaro has the 4L60-E and it cost me $1500 to rebuild it. However, it failed at 97K miles. So the auto tranny in our goats is tried and proven and they last a long time. Just know that when it's time to fix it, it is costly.

I am not aware how expensive the Tremec 6 speed tranny is. It is the same manual found in the Z06 and the Viper, along with a host of other high performance cars. So this transmission is tried and proven as well. If anything is gonna fail first the way I drive, I know it is the wimpy factory clutch.

The 4L60E is prety beefy in the GTOs. It has some components from the 4L65E transmission. If your going to hop a an A4 car Id say get a nice transmission cooler and some new computer tuning to tone down the Torque Managment programming.