For what will you be using the car? The Rav4 is no good off road, while the Vitara is an ancient dinosaur that'll put the Crosswind to shame.

The Rav4 would do fine as a city car though, and the Vitara is an excellent off roader with revered mud plugging and water fording skills even in stock form. We used to maintain a 3 door Suzuki Escudo 1.6A/T in Taiwan before and have been testament to its flood fording capability. It was able to ford floods reaching the windowsills of the car no problem and has an FC of 8-9km/L in Taiwan city driving conditions.
I would always suggest the 5 door over the 3 door for practicality reasons, unless you have no more than one additional passenger 99.99% of the time. The 5 door is very short already anyway.
Here's my take on the two:
Reliability: Both, though the Rav4 should have an edge in the parts department.
Efficiency/fuel consumption: Vitara. No matter how you put it, a 1.6L engine will always be more fuel efficient than a 1.8L/2.0L engine, especially in city driving.
Engine power: Rav4. I have driven a 3 door A/T Escudo before, engine was rather asthmatic though the 160km/h maximum speed indicated in the speedometer is definitely achievable.
Stability: Rav4. Unibody platform will always be more stable on road than a body-on-frame.
A/T or M/T: Definitely M/T. Its a lot more responsive and fuel efficient. Old A/T's tend to rob LOTS of power and think with their stomachs (stupid shifting patterns and heavy fuel consumption).