What are the prices of any accessories/feet? I have the Janome 6600 and love the extra wide throat space. I don't know if the Bernina has that. Since I bought my machine, I have only been back to the dealer once or twice, and I bought it about 3 years ago.
I also found a group on Yahoo just for owners of the Janome MC6600 and have found useful tips there. Usually any glitches are operator error.
Either machine would probably do what you want them to once the final decision is made.