Kay, I have no idea regarding the gearbox differences on Plus 4. Never had a normal Plus 4 myself.
Positive experiences concerning the newer GDI engine have been told here on TM.
The reason I nevertheless personally would vote for the 145 HP Duratec is that this older engine is very popular and was built into many Ford cars while the new GDI is an US engine and so far I know (not proved) in one model only used overthere. It never was used in Europe with a standard Ford car.
The older 145 HP version is durable during the long term and has experienced potential regarding tuning. The dashboard look of the older car is the same as the 4/4 shows it until now.