The few reasons that i know of:
-expensive to maintain
-very limited top speed (some of them are around 50-60mph)
You don't really need to modify the suspension very much. You can run what ever current configuration you have, just modify the brackets on the axle to match your suspension type. Since most portals give you a 4-6 inch lift due to their design, you don't need to run much lift in addition to them.
You can see how the red JK on the right has the axle tucked up about as high as they normally do from the factory. He is probably running very little lift.
Just a few comments from someone who has learned all of this first hand:
1. They are heavy-- but there are lighter options like the Volvo 303's. You don't have to run mog's, but heavy generally does equate to strength.
2. Expensive to maintain? Expensive to build but to maintain I would say that would depend upon how much they are abused. If you are not adding them to a high HP rig that you plan to abuse on a high traction surface-- like rock-- then maintenance is minimal. They can handle a lot of power but not rapid loading/unloading as can be experienced with aggressive driving on rock surfaces.
3. Noisy? Not in the least. They make no more noise than any normal axle. In fact, when they are completely locked up, the operation is actually smoother than a traditional axle with less "hopping" and lurching. They just scrub off rubber.
4. Very limited top speed? Again, not in my experience. The limiting factor is not the axles, but is instead the final gear ratio. I run a little 3.0 Toyota V6 to push my HEAVY rig on 40 inch tires around. I can cruise 70 on the highway easily. Of course the V6 likes to rev. At 60 I am doing 3000 rpm in 5th gear-- about perfect for this motor since it is just entered it's power curve. But it would be hard on a V8 (OK maybe not a Toyota V8 which is in my long term plans) and a diesel is certainly out of the question in this application. A diesel with a final drive splitter would be one solution. It is possible. Point being-- the axles are not the limiting factor. Plus, if you are running portals than you are probably running 40+ inch tires and not spending much time above 60 mph anyway unless you get your tires for free.
Oh, dropped by because I love all things Toyota and would love to have a FJC. But I have a big family-- 4 kids-- so it will likely mean that I will build another 4Runner instead but this time a 7 passenger V8 4Runner mild build on 33's or 35's. Enjoyed seeing you all in Ouray a couple of weeks back. That is just down the road from my place in Montrose and I go there a lot.