I reckon both engines are good, each having it's own pros and cons.
However, TDi 200 is now getting quite long in the tooth and some spares, notably cylinder heads are becoming difficult to get hold of.
Tdi 300 on the other hand is really coming into it's own, spares-wise, so I would reccomend this engine for your project.
Just make sure you get a TDi 300 from a manual-gearbox car, otherwise the engine from an autobox has electronics on it that add unnneccesary complications. Alright as a road-car, but not so good as an expedition vehicle.