Yes, the GX is ~10% heavier and that does impact acceleration. I wouldn't expect much difference in 0-60 between a Limited and an SR5 because despite the marginally higher drivetrain loss of the FT4WD in the Limited, you can mash the throttle and there will be no slippage instead of playing the traction control game with the, for all practical purposes, RWD SR5. The V8 would be tied to a 6AT as well, so you could expect ~130lbs of weight gain* on a V8, 6AT 4Runner.
I'm curious about your definition of "struggle". Yes, the V6 will have to downshift more often than the V8, but there is plenty of power and torque available after the downshift. Driving through WV mountains, I'll occasionally see 3rd gear on the steepest ones but that is still only 3200RPM or so at interstate speeds. It isn't like the V6 has to rev out to 4500RPM for any time unless you're passing. If you're regularly towing 5000lbs over mountains, maybe the 4Runner isn't the right vehicle for you. I'd be more worried about the brakes and short wheelbase coming down the other side.
I'm not so much arguing against more power as I'm arguing that Toyota probably had a hard time building a business case for the V8. The weaker 1GR in the Tacoma tows 6500lbs compared to the 4Runner's 5000lbs. I'm going to wager that the powerplant isn't the limiting factor in the 4Runner's rating. The additional costs in certifying a 2nd version of the vehicle for crash testing may have pushed it past being a worthwhile venture. Then roll in the fact that more sales may have ended up with the lower margin, japan build V8 4Runner instead of the higher margin, local built V8 Sequoia for those that absolutely needed the V8. Toyota
probably made a sound business decision offering only the V6. The 4Runner is a niche product these days.
* I got this number by comparing a base 4x2 double cab 1GR-FE (updated) 5AT Tundra to a base 4x2 double cab 1UR-FE 6AT Tundra.
Toyota Tundra Truck - 2012 Performance and Specifications