Hello everyone, I use a late 2016 touchbar MAcbook Pro with highest specs and I think I solved the issue. At least found out the reason. This Magic Mouse 2 lag thing happens due to interference with USB-C external peripherals somehow.
I am using a Dell U2518D as an external monitor and connected with USBC to DisplayPort Cable. I changed the USB-C port from right to the left side and lag ended. You can try different combinations if you have any external peripherals. It looks like, in my setup, right side of the USB-C ports on my mac does this interference. It hapened with a USB-C multi connection HUB as well.
Please try and share your findings. I really don't want to give up on my Magic Mouse 2 as I am used to it with many gestures.