I've ridden my friend s1kRR, comparing to zx6 (both year 2017), and 1000cc bikes will feel smoother (cruising feeling) at 110-160km/h. You won't feel the bike is working hard, and it can casually cruise at that speed. Actually it's quite obvious that a 1000cc is better then 600 right... (600 will feel "lighter" but the difference won't matter after you've used a 1000cc bike long enough, you'll learn how to get better then a 600 - said by my friend who owns the 1000cc)

If your priority is engine vibration/nvh/comfort - my best advice is DO NOT CHANGE your stock exhaust, or infact any aftermarket parts.
As usual, this is a very personal answer, and most owners of mt09 will say bad things about z900, while z900 will say bad things about mt09 - simply because Malaysians must always justify their purchase, and get their friends approvals. So, you should never make a decision based on what "others" said.

Well but to share my personal opinion during the time of purchase, i already had more then enough disposable unused cash to go for bikes in these price range, infact already tried all these: Stripple RS, zx6 or s1000r(naked). Additionally i have no plan to keep this bike more then 2 years also, so i'm not going to defend z900 also lol.

1. Seating Position, mt09 not stylo enough. MT09 seating position is way too damn straight, it looks very awkward, from far you look like riding an old man's bike (gs1200 comes to mind ahem) But at the same time, i don't want to learn on a zx6/supersports bike as well - lesser handlebar leverage etc. My goal is to get the most beginner friendly yet sporty looking enough as my first ever motorcycle right after getting license.

2. Build quality, mt09 really exudes the "budget bike" feeling. It looks very cheap, i don't feel the refinement in mt09 bike, it just feels like a bike built-up from whatever yamaha had the leftover spareparts for, there is no bespoke feeling in mt09 at all. Furthermore, being the cheapest bike in the category dosen't help (i'm new, and budget is not in my top3 priority, and normally i won't buy the cheapest tier of item, no matter what product range la)

3. mt09 STOCK does not have any wind protection at all. I know this is a stupid point for naked bike category, but comeon i still want some sort of wind redirection or "safezone". Tracer was a no-no, it was way too "big" looking for me to handle as a beginner.

4. Electronics.  If a bike wants to give electronics assist, i really wouldn't trust it from a budget-bike perspective, i much much rather it don't put any electronic assist then putting "budget" e-assists. Also, as a beginner i want to completely feel the raw feeling of unassisted bike so i can learn better.

5. Throttle, ECU mapping. It's just not smooth, and overly done. It's like the ECU is mapped to inject 20%fuel@10% throttle opening. Basically this is what i meant by "unrefined". Almost all other bikes i tested do not have this "rough" throttle feeling. No, i'm not talking about the powerband in relation to RPM, zx6 has an aggressive powerband yet i still feel it's smooth.

That's my thought when i bought the bike 9 months ago, z900 is basically an upgraded version of mt09, even the price shows that. Mt09 is cheaper but it needs to spend some cost on electronics, z900 is more expensive, but zero electronics and all spend on raw refined feeling of the engine and things that matters.