I suspect the reason is extra RAM, 512MB vs 256MB.About a year ago I tried all the 'high end' consumer routers (at the time) BestBuy had, Netgear R8000, Linksys WRT3200AC, Buffalo AirStation 1750, Asus rt-ac3100. I flashed every offical, open source and 3rd party firmware I could find for every router I had but only one combination could pull off all the functions that I needed it to. The Asus RT-AC3100 running Merlin Firmware.
Our home netowrk has 17 wi-fi devices connected, a 24 port switch connected, VPN Client active w/ policy routing, stream movies from the routers usb with a WD mypassport (self-powered through USB 3.0), Netflix streaming in full HD to 3-4 TV's at the same time, tablets phones, online gaming, all mostly over wifi and this thing is like a rock. Never lags or reboots, it's on the 2nd floor of a 3 story home and I get wifi coverage inside and out in the yard no problem.
Merlin runs great on the 3100 and the resource usage is amazing, the CPU rarely goes over 10% and the average RAM use average is about 15%. Only thing I would have done differently would've been to wait a little longer for the 88U to release just because those extra ports could've come in handy!
Can you elaborate what is lacking with R8000?