I gotta say Andi, a lot of that article is full of shit. I feel a lot of it comes from someone who either doesn't have the experience or perhaps the money for a 1000cc bike and has the need to boost their ego whilst riding the smaller bike.
I am lucky enough to have spent a considerable number of years and KMs on both size bikes, commuting, hill riding and track days. These are my findings...
Lets start with the mighty dollar. It costs a little more to buy, run and insure a 1000 at least initially - not a lot different from upgrading your car from a V6 to a V8. Expect Higher fuel consumption, perhaps higher tyre wear as you'll no doubt use that extra power a bit (but ride sedately and it would be the same as a 600) and maybe a couple of $ more to service. However, as a road bike sticking close to the speed limit, the 1L bike will live its life lower in the rev range allowing for less wear & tear and longer engine life. I get almost as many KMs from a chain on the 1000 as I did my 600 - except for the one I snapped, but that was only a few weeks old and I believe was faulty.
Every day riding. Lets face it, the 1L bike is heavier oveall, but mostly has a heavier crank/flywheel. The extra rotating mass makes the bike harder/slower to turn, which on the road simply requires a little more effort to counter-steer. For me, I find the modern 600s are a little too small for my frame and I am more comfortable on the 1L bike. I also find for the commute the 600s higher rev buzz can get on my nerves along with the constant gear changes. Get out into the hills and it swaps a little; the high rev scream is lost on the 1L which takes some fun away unless you want to go into warp. The lighter weight and quicker turn in flick make the 600 a bit more fun too. However, the 1000 ridden well takes less effort for riding the pace in a nice smooth manner.
Get to the track or for key in brain out twisties and each bike has pros and cons. The 600 can brake later, turn in faster and the lower power output means you can really jam open the throttle from the apex knowing your not going to overpower the rear tyre. On the 1000 you have to be more aware of your throttle control, but you can apex at pretty much the same speed at the 600s. Once past the Apex, the acceleration from the corner is a whole other world from the 600. The 1L is more forgiving going in a gear too high, is an absolute blast rushing from a wave to torque into awesome power.
On the whole, both bikes are very capable for many many KMs of riding pleasure. The 1000 requires a little more respect concerning it's speed and power and when ridden hard is more expensive to live with. As for ergonomics, different brands have different set-ups and each generation has it's quirks. I'd say go test ride a whole bunch of both 600s and 1000s and see which bike fits you best. I've done 10hr days on both my old CBR600 and the 07 ZX10 and have no issues on either. I'm just getting into track days on the 1000 and am a little weary of over cooking the power on turn exit, but so far it's been almost as easy as the 600, and throttle jockeys who can't corner no longer pull away on the straight making passing them easier