I've owned and LOVED a handful of Jeeps. My FJ is the first Toyota I've owned. I'm very happy with it.
When I was deciding what to get I weighed all of these same options and choices. Yes there is ridiculous aftermarket support for Jeeps but lets be honest, there is still a shitload for the FJ. Another thing to consider is the availibility of shared Toyota platform products (wheels, control arms, shocks and on and on…). Unless you plan on dropping 50k into whatever rig you decide on, I would just think about it from the most base, practical angle you possibly can. Storage? Family? Long trips? Rock crawling? Camping? What are you REALLY going to be doing with it?
What tipped the balance for me was doing a 6k mile road trip with a friend in his JKU. Not the greatest if you have vast expanses of highway between destinations (especially lame if you have huge tires and a lift IMO). I did a 10k then a 12k mile trip last year in my FJ with a lot of highway / back country driving and was feeling great at the end of each :) Bottom line for me, the FJ handled better on multiple road surfaces with large tires and a lift.
Honeslty though, they both kick ass. You will be happy either way. The grass is always greener on the other side, UNLESS you tend to your own lawn.