I have driven both of these vehicles,
Prado 2004
Prado 2001
Pajero 2004
I owned prado 2004 and pajero 2004 (it was shogun, uk version) and in my experience prado is lot better than pajero, though pajero/shogun was 3200cc diesel and prado was 3000cc diesel but prado had more pulling power.
In pajero you just keep on pressing accelerator and it won't run fast for sometime, it is more noisy as well. That was the reason I sold it two months after buying it.