I don't know much about the Autos, but if you're worried about gearbox strength avoid the 1.6 manual, it has a relatively weak gearbox and was the most likely to fail. (Although not too common anyway)
The 1.8(rare), 2L and GTI (1.8Turbo) have stronger boxes.
Otherwise, there aren't any major mechanical problems - Because most of the mechanics are shared across the entire VAG range (Audi, VW, Seat, Skoda etc) they tend to be pretty bulletproof.
VAG put the 1.8T in so many cars its rediculous, and they still use it to day in the VW Polo and Audi A4. (In Aus, more models overseas)
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