100 or 80? That's not too far from asking 40 or FJ cruiser.
I had a sweet 80, and now I have a low mile 100. It's crazy how many more things the 100's have in stock form. Others have also mentioned, 80's are just getting old. Finding a really good one is becoming difficult and expensive.
Me, I like the 100 better, though I haven't modified yet, so I can't speak to the trail ability first hand just yet, only that others have followed my 40.
Here's a list of pro comparisons from my perspective:
100- (03 & up)
More legroom if you are 6' or taller.
Factory heated seats (hey, don't knock it!)
Power vent windows. Sounds crazy, but just plain convenient.
Ability to actually accelerate into traffic.
Climbs mtns with ease.
Tows trailers with "ease".
Rear a/c for passengers
More legroom for passengers
Headlights are better
All windows power up/down with one touch.
Better gas mileage
Way better brakes
Child seat anchors
Rear power outlet
Multiple front power outlets
Jump seats are a better design
Roof rack mounts don't rust out*
Keyless entry that works from more than 4' away
Engine runs cooler
I'm probably forgetting something.....
80 series ( 97 for me)
Factory diff locks (those were sweet)
Full floater (never heard of a 100 axle failing, but many would claim a FF is stronger)
No factory NAV to deal with
I think the seats were better fitting, though I had less leg room)
Solid front axle is serious beef
Easily lifted (mild lift)
Better air filter
Dual battery potential is easier
Slider windows offer a larger opening
Narrower for tighter trails
And that's pretty much where it ends. Honestly, there is some weight given to that front axle and diff locks, but that's about it. Everything else really is newer and better functioning. Normally, I would say time will tell, but there are now 100's with 400k miles, so they've proven themselves. You can add all or most of the standard features from the 100 to the 80, but you'll spend a fortune and an eternity doing it. So, outside of the width, and solid axle, of the three real 80 series strengths, the 100 is only a compromise on 2. All the other positives far outweigh those two unless you are truly going gonzo family wheeling rig.
That said, I miss my 80 series, but only because I'm a hoarder.