well, some points that seem relevant are
A) the H3 is slwoer than the FJ on-road. to me this isn't an issue because, well, if i'd wanted to go fast i wouldn't have bought a hummer (h2), i'd have bought a porsche
B) the H3 rides better/quieter than the FJ, and i don't give a rats rump what a mag has to say about it.
C) the interior of the H3 is, by a huge margin, nicer than the FJ. especially if you're sporting leather. Go compare the feel and smell of the H3s leather interior to that in a $50k Audi A6. or a $50k BMW 5-series. Oh, wait, that ISN'T LEATHER in those cars, its pleather.
D) the H3s rear seats seem better, at least in my limited experience. neither ones are rolls royce for back seat accomodations. in the H3 rear passengers get their own door.
E) offroad this is a trumping on paper
E1) the H3 has superior ground clearance. i measure 9.5 minimum (better than the hummer spec) with the factory offroad tires -vs- much less with the FJ (go measure it yourself)
E2) The H3 has computer-controlled traction control (akin to the Atrac) + locking center and rear differentials. The FJ has atrac + locking rear only, and those are optional.
E3) The H3s underbody arrangement and protection are far superior to that on the FJ.
F) visibility is worse in the FJ
G) the FJ looks like something my son made with legos. only it doesn't have a cool lego-dude to sort of balance it out.
H) initial test drives show mileage in the FJ well below the EPA suggestions, so its probably no better than the H3, perhaps less, who knows. but, then, i get almost 15 with my H2, so maybe vehicles just vary alot.