This forum section is for the next vehicle generation after that one, but assuming you are indeed talking about a 2005 only (Mk4), then there is NO question - manual!!
We have not heard anywhere near as many failure reports for the 2004 - 2005 5-speed auto trans as we have heard for the O1M 4-speed auto in prior years. It is at this point anyone's guess whether this is really because they are better, or just because they haven't started reaching MTBF (Mean Time Between Failure) yet. The manual, on the other hand, is a known quantity.