I would personally go ABY everytime. The 3B owners will say 'booh - what about coilpacks' but the original items last about 120k miles so thats hardly an issue.
ABY is more technically advanced, has much more torque with factory s/w, has better engine diagnostics/logging if needed. There is no silly old dissy to worry about. The 6-speed box is stronger. It has a superior airbox and intercooler to the 3B and better headlights. The ABY is also much easier to upgrade on the RS2 route if you so wish... But of course those kind or power/torque levels are available on 3B with similar mods and a custom ECU.
Two advantages the 3B has are the lighter flywheel (which can be retrofitted to ABY if you want to give that additional free-revving character of the 3B though you lose some of the silky smooth power delivery on the ABY) and that some are old enough to be legally deCATTed.
http://www.s2forum.com/forum/showthread.php?t=25763