ignition coil

I have been an avid follower of vwvortex in the past and finally had something that made me irate enough to register and ask for some advice. I had a '96 Jetta GLX, stock except for K&N filter that ate ignition coils like made. Went through 3 of them in 2 years. So I decided to upgrade to a '00 GTI VR6, hoping that vw finally got the quality right. Well, yesterday, after a few days of rain, I hoped into my car to go home and it was sputtering, farting, no power. The check engine light came on and thankfully the local vw dealer could work me in (friday 3:30). They said it is probably the ignition coil, which is what I thought it was to begin with. Has anyone had any trouble with ignition coils and does vw know about it? I know the Mk 3's had probs, but figured vw changed the design. I am a avid vw fan, but I am seriously considering changing brands when I can next afford a new car. Don't want to go Japanese, but may have to seriously consider a WRX STi in 2003-2004, if I can swing it.
Thanks,
Chris
'00 GTI VR6. Satin Silver K&N airfilter, BFG g-Force TA's.