We considered a new Pro-4X when we were looking. Decided on the 4Runner for several reasons:
1) Seats not as comfortable. Big negative since we have family 12+ hours away that we occasionally go visit. And we like road trips too.
2) Entry to back seat is very narrow. Difficult when our aging parents visit and we need to chauffeur.
3) Less cargo area for trips. Less room in backseat for passengers.
4) I did read Nissan forums, and found the previous gen tended to have more issues. The overall opinion of reliability with Toyota (based on what I read in Toyota forums for Toyotas, and what I read on Nissan forums for Xterras) was significantly better than the Nissan.
5) 4Runner could be had with a sunroof. Not an option on any Xterra.
I will admit, if I were single and didn't care about passengers, and wanted a cheap offroad SUV, the Pro-4X would be a contender. I did like the throttle response that engine had (pretty similar to 4R, IIRC) and the handling for a narrow, top heavy BOF SUV wasn't that bad. It was a fun little ute on the test drive. I kinda liked the look of it too. But in the end, the 4R won out, and we've been very happy with that decision. Absolutely no regrets.