I currently own 2003 Nissan Pathfinder SE 4x4 and have to say that this is a great vehicle and was troublefree for me.
It's comfortable, smooth, capable (handled well in mud and snow) and reliable.
It has automatic climate control and BOSE Audio system.
I use it as a family vehicle, I don't tow but haul some heavy cargo several times a year.
When I was choosing between 3rd gen 4runner and my car 4runners were 1000$ expensive. I'm happy I chose pathfinder because it's a beautiful vehicle, has enough ground clearance for me, comfortable and reliable.
I don't have any problem with my car but already looking for a good replacement, because I love to plan ahead.
Until now my favorite was 4th gen 4runner and the last 3 years I've been browsing this forum everyday

4runner is a pretty vehicle (rear end not so much) and technically is advanced than my current car on every front, BUT more I read this forum, more I fear to have problems with either frozen calipers and/or 4lo actuator switch. I don't live in USA, I won't be under warranty and I definitely know those repairs will cost me an arm and a leg.
So after that I started looking at current gen pathfinder and recently at 5th gen 4runner.
Looks: Both are ugly vehicles. pathfinder's designer probably was on drugs when designing the rear of the vehicle. It's just a box, no esthetics. And compared to 4th gen 4runner, 5th gen is a complete disaster. Of course both vehicles grow on you, but initial reaction is puke.
Features: I don't consider leather interior, because don't find any advantage over cloth (If someone enlighten me, I will be glad). So If we compare SR5 4x4 to SV 4x4, pathfinder beats it with ease. SR5 lacks automatic climate control (which is a must in my case and shame to toyota that they downgraded it from previous gen.) and rear view camera as a standard equipment. Pathfinder has dual zone climate control + Big screen rear view camera, but you cannot have bluetooth unless you upgrade to Silver Edition.
On the other hand SR5 can be equipped with in-mirror backup cammera+blue-logic bluetooth or a more advanced bluetooth+mp3 with usb.
Pathfinder has standard 3rd row seats and bigger interior but second row seats are designed for children in mind only.
Reliability: If we consider that pathfinder is at the end of the generation it's quite reliable. 2005-2006-s have some radiator problem and up until 2011 vanos system could develop a whine because of plastic tensioners. If you buy MY 2011 pathfinder it probably be more reliable than 2011 4runner, because 4runner is a new model. Also as others mentioned in other threads I don't think frozen caliper issue has gone away.
In summary If I had 35k today and you ask me what car should I take, I would take pathfinder, because It has more features, is (sufficiently) reliable and I can compromise on the looks.
But It would be better to wait a year or two and see what 4runner redesign brings to us. If frozen caliper issue is admitted and fixed, automatic climate control is standard and the vehicle's style is refined, that would be my bet.