Great points all around...some thoughts in answer (not original order, but in the current "thought order" lol)
-Chain...When a shaft drive bike takes 2 consecutive podium finishes in international open competition I'll consider listening to crap about chains..until then, I'm thinking it's maintenance laziness talking
Oh yeah...the 1000RR that the BMW guys love to point out as the top of the sportbike pyramid...shaft??? Nope.
-Exhaust...yeah, not a power thing. Reasonably today's bikes don't really gain anything from new cans (unlike tuning the expansion chambers on two strokes). Can make a weight difference but really it's for looks or sound. I don't really like the sound the Ninja makes, which is not a big deal and thus way down the priorities list.
-Suspension...the front suspension on the Ninja is already three way adjustable with plenty of "clicks" available, and the springs are both plenty stiff and progressive. Thus, not in a rush to change it just because of a change to the rear. From the factory the front end of the Ninja is better sorted than the rear, the front end components come directly from the ZX sportbikes, the rear end was bespoke to the Z1000 and not in the same league. It's difficult to get set up right while maintaining both enough effective travel and good compression characteristics. In day to day riding there's no reason to really change the rear unless you are far outside of the range of adjustment. I'd like to take it to track days though and the rear can get a little spooky in certain circumstances. Quite common in the Ninja1000 world to just do the back. The most common mod to the front is not actually a suspension change but to drop the forks 5-10mm in the triple clamp to alter geometry and quicken initial turn-in and increase front end feel. If I were ever to change the front it would really only make sense to change it all, i.e. put in new cartridges etc. If it ever gets to that I would simply use a different bike.
Regarding the Penske/Ohlins/Other choice, it came down to the construction of the innards and overall adjustability, including easy ride height adjustment. The spring is largely irrelevant because you can always get whatever is the right spring for your weight and purpose separate from the shock body. Since coming out worldwide there is now a pretty good base of bikes who have had suspension mods and, so far, the Penskes get great marks - although more expensive than the Ohlins.
Brakes...As with the motor, power is not in question. The pads and steel lines are to address specific "feel" preferences. The steel lines will improve the feel at the grip, giving a more linear pull with more direct cause/effect as the lines won't flex under pressure. Of note, I don't expect huge gains here as in bikes of the past because all the lines on the N1K are stout and shielded. The pads are to improve, or maybe change is a better word to use, the initial bite and progression. With the stock pads the brakes are certainly strong enough and actually are already pretty progressive and fade free. I personally like a bit more of an initial bite, somewhere between one and two finger brakes. Just going to a slightly more grabby compound will take care of that.