There are many more differences between setups 1 and 2. Those AiMesh-connected XT12s don't inspire confidence in me that it is (just) the GT-AX11000 that may be misbehaving.
Have you performed a full network reboot via the GUI; AiMesh, System Settings, System Reboot?
Have you performed a full power shutdown/electrical reset (pull the AC power plugs from both the routers and the wall plugs, and wait for as long as you can; minimum of 2 minutes (I would aim for 10 minutes or longer, including unplugging the ISP ONT/modem too for at least that long), leaving all the power switches 'on', before powering everything back up again)?
Have you turned off the XT12s and seen a difference in the Gui's responsiveness? If simply turning them off doesn't do anything, have you tried removing them from the AiMesh setup, to test?
Have you performed a full reset to factory defaults on the setup 2 GT-AX11000 lately?
After doing a full system reboot, wait for at least 10 to 15 minutes for the routers/network to fully settle down. Then, on the main router, create a backup config file. Disconnect everything from the main router, including USB devices and the WAN port connection to your ISP, and perform a full reset to factory defaults using the reset button, WPS button, or via the GUI. Better yet, do all three. In between, reflash the firmware that is already installed now.
Import the saved backup config file you created and re-associate the AiMesh nodes (XT12s). Test if the issue persists. If it does, I would redo the full reset to factory defaults, and then minimally and manually configure the router to secure it and connect to your ISP. Test. If satisfactory, add one node, test again. Continue building your network to where it was (manually, keeping good notes of your progress), until it is either fully working, or, it shows the same symptoms. If the latter, come back with those details and we may be able to help/diagnose further at that time.
Thank you for your detailed instruction. I did try to reboot the setup 2 gt ax11000 with the power button and also via the admin page few times.
After reboot for first few mins things are fast but then after a while the admin page started to lag again. I haven't try to reboot the nodes as the 2x xt12 nodes just auto connects every time the router is rebooted.
So far everything is running stable and fast it's just the web GUI is extremely slow when I try to login and change settings.
my setup 1 GT AX11000 router is running flawlessly uptime is over 22days I think and the web GUI is fast as well.
I haven't reset to factory default on the setup 2 AX11000 for few years. as it's been running fine with Merlin. even on the 388.1 ROG firmware everything else works fine except the slow web GUI. Because I've many custom settings on the setup 2 ax11000 atm with 2 VPN connection and 1 VPN server running also connected to a unifi 10GBE switch and connected to a Synology NAS all running 10GBE connection and fixed IP. even the 10GBE connection is getting full speed as well.
The AXE 16000 I ordered should arrive in the next few days when I receive it I will do a clean install for everything and then install the 388.1 firmware and see how it goes.
also another interesting problem is on the setup 1 GT AX11000 logging in with the IOS Asus app it load fast and can see all devices connected to it. about 30 clients atm.
but on the setup 2 GT AX11000 when logging in with the IOS asus app. it is showing only 3 devices which are the router and the 2 nodes but unable to see details of all other 50 clients. some times it will show up after waiting for few mins sometimes it won't. But all wifi and lan devices are working at full speed and stable. the only problem is just the slow web GUI When I need to login and change settings.
I will report back once I have the AXE16000 setup with the 2 nodes and all the extra custom settings. I will do them manually 1 by 1 instead of restoring settings from the ax11000.