RT-AX88U Pro has 2x 2.5GbE ports, 4-stream 2.4GHz radio, 4-stream 5GHz radio, 1x USB port. Larger footprint flat design.
RT-AX86U Pro has 1x 2.5GbE port, 3-stream 2.4GHz radio, 4-stream 5GHz radio, 2x USB ports. Smaller footprint vertical design.
You are more interested in Wi-Fi 6 performance and it usually means on 5GHz band. The performance will be about the same. Both routers have the same CPU, RAM and 5GHz radio with the same SDK firmware and Broadcom drivers. The 4th antenna on RT-AX86U Pro is internal, but with the same dBi as external antennas. If you don't need 2x 2.5GbE ports - this is the more compact model, popular around, Asuswrt-Merlin supported. Usually cheaper as well.