is the navigation in the GTI better than aftermarket? What if any problems with the car in general?

Answer 1

After market GPS systems are ALWAYS better then factory stuff.

1) More bells and whistles - newer units now play your ipods, answer your phones, even tell you about speed cameras
2) Easier firmware upgrades - free over the internet vs. the $60 dealer charge
3) Easier map upgrades - and if you use it to go to restaurants or other facilities this is important. Try finding a gas station in the middle of nowhere only to discover it closed two years ago (been there sweated THAT one out).
4) Portable, cars, motorcycles, etc.. even bicycles - same unit, different mounts.
5) Less theft - it goes indoors with you instead of being a big hole in your dashboard the next mornng.

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Answer 2

Yes, the fact its not a cheap unit stuck in the window makes it better for me at least.

The RNS-E and later VAG navis are very nice, I'd get it in a heartbeat. It too has many "bells and whistles" and plays mp3s off memory cards and such, integrates with the rest of the vehicle electronics etc.