The 32.5MP APS-C crop 90D will have the advantage in most cases.

The 26MP full frame 6D Mark II would only be an advantage if you....

....need to use very high ISO for some reason. 6D Mark II's considerably less "crowded" sensor will be able to shoot at higher ISO before heat gain and cross talk cause noise problems in images. I haven't seen DXO tests of the 90D yet, it's too new.... but I have little doubt the 6DII will have higher usable ISO. But, shooting macro, you're not likely to need super high ISO very often. With any camera, shooting macro you would be better served either using longer exposure when the subject allows, with a tripod if necessary, and/or using flash to illuminate the subject.

....or if you will be making very big enlargements from the images. In that case, the 6DII's images that need less magnification have the potential to hold up better. However, you probably won't see much difference until you make prints larger than 13x19".

If you are going to go to the trouble of "full frame", I'd opt for a higher resolution camera than the 6DII. Canon 5D Mark IV with 30MP or 5DS-R with 50MP would make more sense. (The 5DS-R has very limited high ISO, by the way.)

But if you're going to spend this kind of money for a special use camera, why stop with "full frame"? You might want to consider going even bigger with a medium format digital camera. It used to be that this next step up in sensor size was cost-prohibitive, but prices have come way, way down in recent years. Fuji, Mamiya, Pentax and even Hasselblad are all now offering moderately priced MF digital. Sure, these are a bit more expensive than a Canon or Nikon full frame camera... but not all that much more.

A 50MP Canon 5DS-R body costs $3699 and a Canon EF 100mm f/2.8L IS USM lens is currently on sale for $699 (normally $900), plus $172 for the separately sold Tripod Ring D.... $4570

A 50MP Fuji GFX body currently costs $4000 and the Fuji GF 120mm f/4 Macro OIS WR lens is on sale for $2200 (normally $2700).... $6200.

Used to be that MF cameras cost as much as a new car (and some still do). But prices have come down considerably, at the same time performance has improved.

Practically speaking, cropping with a computer offers more precise control, but I would bet most crop sensor images still get a final crop for composition in post anyway. To the main topic, unless the OP refers to crop as smaller sensors with interchangeable lenses only, consider the fixed lens compacts with good lenses, such as Canon GF or Nikon P7000 series, as an alternative to FF for close-ups. Their smaller size can help getting closer to the subject in tight quarters and still have adequate IQ. Getting in close also can mean less cropping with the computer.

I'm not following. Macro is 1:1. If I take a photo of a fly sitting on a white piece of paper. At 1:1 magnification how is one a macro and the other not? The fly is the same size on either camera's sensor. The FF will have more of the paper captured on it's larger sensor. Upon printing the full images to the same paper sizes, those photo's will be visibly different, but why would one be considered a macro image and the other not?

And if i'm taking a macro 1:1 of a larger flower (or perhaps a nickel), the FF camera may very well fit that entire flower (or nickel) at 1:1 on it's sensor, while the cropped sensor could not. Again if both are at a 1:1 magnification, why would one image not be considered a macro?

Perhaps your definition of macro is not 1:1? Subject size matching image size on the camera's sensor.?

So what's better for 1:1 Macro photography - FF or cropped sensor, I'd think it would depend on the size of the subject being photographed.

Perhaps, I'm misunderstanding what you mean by the exact same picture? - same 1:1 magnification or same content captured?

Practically speaking, cropping with a computer offers more precise control, but I would bet most crop sensor images still get a final crop for composition in post anyway. To the main topic, unless the OP refers to crop as smaller sensors with interchangeable lenses only, consider the fixed lens compacts with good lenses, such as Canon GF or Nikon P7000 series, as an alternative to FF for close-ups. Their smaller size can help getting closer to the subject in tight quarters and still have adequate IQ. Getting in close also can mean less cropping with the computer.

Grahame;
MY POINT EXACTLY.........DOF!!!!!!!! of course the obvious add-on's are COMPOSITION & LIGHTING.
And let us not forget perhaps the most important one of all, THE PHOTOGRAPHER. After all, the beauty of photography as with all art forms is the inspiration and sight of the one who created it.

I hadn't realized that you'd been appointed the defacto standard of acceptable and not acceptable macro photography. Ever thought that there may be some who find your work, lacking, boring and perhaps even un-inspired.

Grahame;
MY POINT EXACTLY.........DOF!!!!!!!! of course the obvious add-on's are COMPOSITION & LIGHTING.
And let us not forget perhaps the most important one of all, THE PHOTOGRAPHER. After all, the beauty of photography as with all art forms is the inspiration and sight of the one who created it.

I hadn't realized that you'd been appointed the defacto standard of acceptable and not acceptable macro photography. Ever thought that there may be some who find your work, lacking, boring and perhaps even un-inspired.