Since the demise of the Xterra and the BOF Pathfinder, Toyota 4Runner sales have almost doubled. (At just over 100,000 in 2015) The loss of the FJ can be factored into that too, but not as much of an influence as Nissan dropping the Exterra and changing the Pathfinder to a crossover.
The fact is Nissan cannot afford to chase a niche market, Toyota can.
Look at the sales of Ford Explorers since it became a crossover, they are everywhere, selling over 200,000 units a year.
It is sad, but vehicles that fit into the "overlanding" market are not currently a profitable market for manufacturers.
Even Chevy and Ford have no midsize BOF players in the SUV market place right now.
Selling 100k 4runners a year isn't really a niche market IMO.
The market for BOF SUV's and trucks is out there. The Wrangler sells very well still, despite minimal changes/revisions. Ford, Chevy, and Ram don't sell unique BOF SUV's, but they do dominate the pickup market and their sales are well beyond the niche market as well. If Ford or Chevy wanted to, they could use those pickup frames and chassis to build SUV's as well, which they have done in the past, and continue to do to some extent. Also, there is rumor from Ford about the Bronco coming back.
The problem isn't that the market demand is shifting away from BOF SUV's/trucks. The crossover has been around for quite some time now, and if the big manufacturers truly saw no financial incentive to produce BOF trucks/SUV's, they would have stopped by now. The issue is that some manufacturers are struggling on how to meet consumer expectations. The F-150, or the Tacoma, or the current 4runner, don't sell well because of best-in-class fuel economy, or ride quality. They sell well because they're rugged and reliable, which is what those types of buyers are looking for.
Nissan seems to have struggled with their marketing. They flip flopped back and forth on whether their Pathfinder was supposed to be a hardcore, off-road capable BOF truck or a unibody, nice handling crossover. Even their last BOF Pathfinder version seemed to be a compromise of sorts with independent front and rear suspensions.
The Xterra actually sold fairly well in its early years, but Nissan essentially kept it the same for 10 years straight and by the end of those 10 years, its sales numbers had dipped a lot, which is to be expected. I never really had much of an affinity for the pathfinders, at least the newer ones, but I always thought the Xterra was a great 4x4, especially for the price point...it's a shame Nissan didn't try to restart/revise that lineup.
IMO, the BOF trucks/SUV's sell just fine in today's market, but only if the manufacturer fully commits and makes it a robust 4x4, offroad-capable vehicle. The minute you start watering it down and trying to make it more "refined" and enjoyable for soccer mom's and daily commuters is the minute you start losing your market share. Crossovers are a dime-a-dozen nowadays, BOF trucks/SUV's aren't, so people who buy them want the truck experience.