Pros for the MINI 'vert would be a semi-useable rear seat for when you need it, better mileage if that matters, fun to drive. Be aware that the first gen convertible carried on until model year 2008 I believe, so the first gen II 'vert would be an '09 model even though the gen II coupe came out in 2007. Lots of debate here, but having owned both, I prefer gen II.
The only way you're getting a gen II TT roadster with manual is finding a 3.2 VR6 equipped one, all 4 cylinder gen II TT's in the US have been DSG. It's also a fun car to drive, has sporty handling, and I think has a higher build quality.
If I only needed two seats, I think I'd try to find a nice low mileage 2008-09 TT 3.2 roadster with manual.