Here's the poop on the 3.0 - some of them came off the factory line with bad head bolt torque, leading to blown gaskets in the first couple years. This was the reason for the recall. By now, any 3.0 that came off the line with bad head bolt torque has either been recalled and fixed, or had the head gasket blow and been fixed. But that's not the end of the story - the reason 3.0s are still blowing head gaskets anyway is due to the exhaust crossover coming a little close to the head, and over time cooking the head gasket right by cylinder six. This can be fixed by wrapping/insulating the crossover, or installing aftermarket headers. So don't be scared of the 3.0 blowing a gasket for no reason - the reasons are in fact well understood and preventable. Personally, I'd avoid the 3.0 for being such a PITA to work on though. One look at the mess of vacuum lines under that hood and I quake in fear. I'll take a 5vze or 22re any day over a 3vze.
Second Gen - 22RE or 3VZE, torsion bar front end is super easy to get as much lift as you want, the front diff is much easier to regear, obviously you're not going to pay as much for the truck. Third Gen - 5VZE or 3RZ (both of which are more powerful than their predecessors, and just as reliable as the 22RE), front suspension is a better configuration for ride comfort but a little more expensive to get moderate to high lift from, bonuses like a factory elocker or a multimode case are available, the interior is a little more refined, etc.
Dimensions-wise, the 3rd gen is just slighty wider and longer than the 2nd, and at stock height sits just a tad lower, not really enough to make a difference. There's more aftermarket offroady goodies available for the 3rd gen, but they'll generally cost more. There's also more bolt-on performance mods for the 3rd gen motors.
I can't think of any other major differences. Really, it comes down to your priorities and what deals you can find to get you your bang for the buck. If you're going to really abuse it on the trails, I'd go with the second gen for sure. If you plan on logging lots of highway miles and will only see moderate offroad, I'd wait for a deal on a third gen. But you can't really go wrong with either as long as you're smart about what truck you buy. Good luck with your search.
