I have both in my stable. Here are my thoughts, bet you've seen some of this with the FJC vs. 80:
The two biggest differences I've seen are MPG (FJ wins - even with it being moderately built) and cargo (100 wins hands down).
Both are worlds better than my '00 Tacoma XtraCab with the 3.4L moderately built (sold years ago but missed).
Others:
I love my FJ but two doors are a PITA with kids and a Lab.
I only have 42K miles on my FJ and haven't had any services issues to date. It will be interesting to see if it has some of the annoying quirks of the 100 at 122k miles.
If Toyota built a four door FJ I'd buy it in a minute.
Visibility from the cab in the 100 is much better than the FJ due to the lower belt line of the 100. You get used to driving blind in the FJ. It isn't that big so you quickly build confidence in your senses.
DIY oil changes are much easier on the FJ with the top mounted oil filter. Interestingly, the take the same OEM filter.
Seems to be better aftermarket support for the FJ.
The FJ is noisy. Lots of owners install DynaMat. I haven't.
The 100, even with AT tires, is quiet and smooth riding. My FJ with the OME sport shocks and mild springs (2") rides ok but can be a bit tiring at times. However if you can leave the FJ stock (who does that?!) it rides very well.
The 100's 2uFZE is a legend but the FJ's first gen engine is no slob either. V8 acceleration in a V6. So much of the FJ drivetrain comes out of the Tacoma or Prado.
The creature comforts of the 100, even mine being 12 yrs old, are better than the FJ. Maybe the newer FJ's offer basic items like sunroofs?
Many of the '07 and '08 have "hidden" ATRAC! Meaning the earlier (later?) models came with ATRAC prewired but no switch. Order the switch online and snap it in and you have ATRAC in 10 minutes or less! Read the FJ forums - the mod is in there and I did it! INCREDIBLE!
The range of the FJ isn't a confidence builder unless you stick with OEM size tires and no lift - but again who wants to do that?! Adding an aux tank is big bucks.
I love both of my rides but the comfort and cargo of the 100 equates to it being used the vast majority of the time. That said, I'll never sell my FJ.