One thing I like about the Pathfinder is that it doesn't have the plastic clip on flares and side body cladding like the 4Runners do. If the flares or body cladding get bumped they break loose where the clips attach and usually have to be replaced. They are big $ and also require painting.
I think mechanically the 4Runner is a little better than the Pathfinder.
I have a pretty long list of silly things that have gone wrong on my Pathfinder. Nothing major it's more annoying than anything.