I have owned both 2.7 prado and diesel Fortuner. I had a 2011 prado TX-L. Sold that last year and this year bought a diesel Fortuner. Can tell you pros and cons of both.
Prado.
Pros
-More presence (can be facelifted etc if youre into that sort of thing)
-Better suspension ( although imo its only slightly better. A lot of people overemphasise this)
-More comfortable seats
-More overall features (esp in the TXL. Sunroof electric seats etc)
-Better grip at higher speeds
Cons
-older model
-interior feels quite dated (leather seats wear out quickly)
-No rear AC cooling esp in 3rd row can be a serious issue in the summers
-2.7 is quite underpowered ( This was the dealbreaker for me) coupled with a 4 spd transmission it feels super sluggish and even dangerous when overtaking
Fortuner
Pros
-2.8 diesel engine is satisfactory. Can be further improved with unichip etc.
-brand new or almost new
-better infotainment system (english instead of japanese)
-Better fuel economy
Cons
-suspension not as great as prado (although not bad at all
-seats are a bit hard and uncomfortable
Once again for me the 2.7 was just way too underpowered and I got rid of it.