The 3.2 VR6 engine uses about 30% more fuel than the 2.0T FSI engine.
The S3 engine is far more tuneable.
The residuals will be much stronger on the S3.
The S3 will handle much better than the A3 3.2 Sport
Top Gear are giving BS, if they think that the 3.2 would handle better than the S3, the VR6 lump weighs much more than the 4pot turbo lump!
OK, the VR6
may sound slightly better - but sound doesn't mean faster, nor more economical, nor better handling. A Milltek on the S3 will soon alter the engine sound!

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Sean - Independent Motor Vehicle Technician (retired)
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'07 Audi B7 RS4 quattro saloon 4.2 FSI V8 32v (BNS) (with ceramic brakes) - WOW
'06/7 VW A5 Golf Mk5 GTI 5dr 2.0T FSI (BWA) DSG, fully loaded, colour coded,
'98/9 Honda CBR600FX, the blueberry trifle
'03 Audi B6 S4 quattro saloon 4.2 V8 40v (BBK) 6sp manual, fully loaded (gone, but not forgotten)