Old thread but it's one of the first to come up when I googled "Asus RT-AC68U cpu 100%". I registered an account here just to post my solution in case it helps someone in future.
I noticed on the WAN page that "Enable VPN + DHCP Connection" (under the "Special Requirement from ISP" section) was set to "Yes". I changed this to "No", hit apply and the router's CPU usage immediately dropped drastically.
I don't know whether this setting was always "Yes" but the problem only occurred today. I'm with Bell Fibe btw.
Prior to this, I checked to make sure that all of the usual suspects were disabled: Wifi auto-channel, QoS, AiProtection, VPN server
Oddly, my 5GHz wifi was set to "Auto" when I had previously set it to a specific channel. At some point this setting defaulted itself. I've noticed this behaviour in other settings from time to time.
The VPN server was also on so I turned it off. Again, pretty sure I'd disabled it in the past.
Neither of these had any impact on the CPU usage as far as I could tell. I was only checking VPN settings because I had an odd looking log entry:
Sep 7 11:54:33 pptpd[4587]: CTRL: EOF or bad error reading ctrl packet length.
Sep 7 11:54:33 pptpd[4587]: CTRL: couldn't read packet header (exit)
Sep 7 11:54:33 pptpd[4587]: CTRL: CTRL read failed
This is what made me notice the "Enable VPN + DHCP Connection" setting. Otherwise, I may not have ever tried disabling it.
Anyway, that's probably more info than needed but just wanted to provide some context as to what led me to this solution. Hope this works for you!