Word Jasamb!
Sure the "best" way is to start on smaller cc bikes, but it is not impossible to learn on an R6. I started in the MSF course and it wasn't too bad, we only went 20mph. I didn't have good practice with working the clutch so that took some practice. The first thing i've notice when i went home and hopped on my dad's suzuki gs500 from the 250cc bike in the MSF was that it was harder to manuver (probably because it was heavier). of course i'm talking about low speeds, which is all you do in the MSF.
My dad sold the gs500 and got a 93 Honda VFR 750. There was a tremedous difference in handling, comfort and of course power. On the GS500 i had to work a lot harder accelerating and turning than on the VFR. The VFR handled a lot more smoothly and because it was so damn heavy it was hard to move around when parking and moving it around with the engine off, but on the freeway it didnt get blown around and it felt more stable and glued to the ground "like a fat guy that can move!" This thing felt like a spaceship compared to my R6. Another thing i did alot when i was learning was i lost my balance at times. I saved most of the falls but i did go down a couple time... No shame, it happens to everyone.
so then i finally get the R6. The gs500 to the r6 is like going from a old ass (plastic bumper) corolla to a 2003 cellica. the VFR, being a sport touring bike is like accord or camry because its more comfortable and handles "ok" whereas the R6 is the sport model and drives like a sport model does. The R6 has sensitive everything, throttle, handling, and braking. In my opinion a lot of people think an R6 is to sensitive for new rider so they should get a slower bike and build skill first before the bike will even let them go fast.
I say just be careful and take things slow and dont think your skill has improved, know if it has. A lot of people think they are better than they really are and thats probaly why they crash.