These two cameras were announced simultaneously, sharing a press release. They share the same imaging sensor, the same processor, and the same image quality.
As can clearly be seen in the overlay comparisons images shared here, the 90D is very considerably larger than the M6 II. The 90D takes up much more space but it provides a considerably larger grip that is comfortable to hold for long periods of time and gives the photographer better control of larger lenses. The optional BG-E14 battery grip provides even more control for the 90D. The M6 II is considerably lighter, weighing just over 1/2 as much as the 90D (12.7 vs. 24.7 / 361 vs. 701g).
The 90D has an optical viewfinder with speed-of-light response time and conventional phase detection AF in addition to the same live view sensor-based AF capabilities found in the M6 Mark II. The 90D requires an LCD loupe for electronic viewfinder (EVF) capabilities while the M6 II has a hot shoe attached accessory EVF, the EVF-DC2, available in addition to an accessory loupe.
Using the optical viewfinder (OVF), the 90D tops out at a 10 fps continuous shooting rate that seems fast until compared to the M6 II's 14 fps capability. Far surpassing that rate is the M6 II's 30 fps burst and preshooting, essentially shooting in the past. When using the optical viewfinder, the 90D has a faster shutter speed available (1/8000 vs. 1/4000 sec.) though both cameras can do 1/16000 sec. when using full electronic shutter. When using the OVF, the 90D has a far higher battery life (1,300 vs 305 shots at 23°C, AE 50%, FE 50%) with a 6-level battery indicator vs. 4.
The controls featured on these cameras are quite different. The 90D has a higher button and dial count but the M6 II has a solid set of controls. The 90D has a joystick while the M6 II features touch and drag AF when the optional EVF is installed.
The 90D has water and dust resistance specified while the M6 II does not. The 90D has a headphone port to its advantage. The 90D's LCD has anti smudge coating while the M6 II's LCD does not. Neither has anti reflection coating.
The 90D has a more powerful built-in flash of GN 12 vs. 4.6 (ISO 100, meters) with a 1 second faster recycle time (3 vs. 4 seconds) and a faster flash sync rate (1/250 vs. 1/200 second).
The M6 II's EF-M lens compatibility is an advantage. However, this camera requires an adapter for use of EF, EF-S, TS-E, and MP-E lenses.
For many people, either of these cameras will be a great choice and some will find that owning both cameras makes perfect sense. It is also likely that there will be one or more significant differentiators in the above list that creates a purchase direction.
Those photographing fast, erratic-moving action will likely prefer the 90D's optical viewfinder yet those same photographers may prefer the M6 II's faster frame rate. Those using large lenses will prefer the 90D's grip size as will those spending large amounts of time with the camera in hand.
That said, those carrying a camera for long periods of time will appreciate the M6 II's lighter weight. Travelers will love the M6 II's small size and light weight as will anyone able to utilize the compact (and excellent performing) EF-M lenses. If one or more EF-M lenses are ideally suited for the subjects, the M6 II is likely the best choice. Those carrying a camera in case an opportunity arises will appreciate the M6 II's compact size.
Again, for many people, either of these cameras will be a great choice and owning both cameras can make perfect sense.