I have heard many complaints about CVT, but has anyone had a good exp with it? Also, what is the best way to prevent some of the common CVT issues that come up?

 

I guess do all the maintance + dont be hard with it

 

There is nothing you can do to help prevent CVT failure, there have been several different design flaws and TSB's to deal with them. Most of the TSB's require major work or overhaul.
Changing the fluid every 40k is a must also, the CVT can develop a lot of debris in the fluid that needs to be changed frequently.

 

What is a TSB?

 

Also, my car has 55K on it, and as per the service records, at 35K the transmission controller? was changed. The tech told me this was a good thing, any thoughts?

 

A TSB (technical service bulletin) is issued by audi to aid in fixing common issues. In the case of the CVT there are about 4 major re-occuring issues, all of which are no easy or cheap fix.
Changing the CVT controller or TCU is one of those TSB repairs which would have cost you around $2,000 if you paid for it. I would sell that POS before it gives you anymore headaches.