My two cents,
nsman, thanks for the great info on tire size and aspect ratio. Even though actual tire height can vary depending on manufacturer. The michelen S-12 is about the lowest profile of 90/90-21. At least that has been my experience in searching for a low profile tire recently.
And I totally agree about the stock tire size having been thought out by the engineers.
I recently went to the mich 90/90-21 S-12 front, and 140/80-18 rear on my 2004 550. The tires seem to work pretty good, although I suspect there is some knob roll over on the hard terrain that I ride on, but, on the soft stuff they work well.
My tire of choice for riding out here in the desert's of Souther California has been the Pirrelli MT18. I find that they not only work good in sand/soft conditions, but, also work well in the hard pack and rocks. And speaking of rocks....... The size and type of MT18 I run is the Heavy Duty, 100/80 front and 120/100 rear. These tires have a tall side wall that is relatively stiff to prevent pinch flats. I run these tires at 12 to 13 psi cold front and about 11 to 12 psi cold in the rear. I also run that green slime stuff in my heavy duty bridgestone tubes. Yeah it's a pain changing tires with those 4mm thick tubes, but, I only have to do it when the tires are worn out
You just need to do a littel experimentation to find out what works best for riding and your pocket book. Those michelins work great, but, they're kinda pricey. The pirrellis work good and they're easier on the ol pocket book. And I have friends who really like the Kenda Carlsbad, they wear good, and they're pretty cheap. Another friend of mine runs the Maxxis IT tires and he is happy with them.
I have been experimenting with different tires for a while and I think that the Pirrelli's are the best working, price friendly, and flat negative tires around.