It depends on where you travel and what type of driving you do (including distance), your style of driving and preference for turbo punch and low down torque or a rev happy engine.
All units have their pros and cons; TDIs offer low end grunt, ability to short shift, ace fuel economy and low tax for example. The 1.4 petrol is agile and nimble and suits round town driving predominantly, but is capable as a motorway cruiser too, though lacks aggression if pushed too hard. The FSI, in my opinion, is a capable short shifter (lacking torque compared to the diesel), but when worked offers a spirited drive. The petrols gear boxes are also the smoothest to engage from my experience. The FSI is also capable of 50+mpg on a run.
FSI and TDI90 carry the lion's share of mechanical reliability issues, but a good well cared for and regularly serviced example may give you many years of happy motoring.
I'd recommend a test drive in the common variants to inform your decision making, unless you happen to find your ideal car first time.
Good luck with your search and don't be afraid to ask as many questions as you need to.