New owner of new '16 RT.
Regarding my experience with the big neutral to 1st shift clunk. Yes it's a pretty big one. Bike actually jumps a bit. However, on mine, when you start from a cold engine. There is zero soft clunk from N to 1st. As the bike warms up, the clunk gets progressively worse to the full on KLUNK when the bike is @ operating temp.
So I've concluded that the problem is within the clutch pack. Maybe the brand/type of oil. I'm @ 200 miles so far and I've noticed the CLUNK was worse for the first 100 miles.
I was wondering if the clunk reaches an acceptable level as the miles accrue.
As far as I surmise from reading myriad comments about this, the N to 1st clunk is fully baked into the 2014-16 models, but as you aptly noted disappears only when the engine is cold AND ambient temp isn't over maybe around 62F or so. As the entire bike warms from ambient the clunk manifests. My sense is everything just expands a wee bit as temp increases. The brand and type of oils that otherwise meet the required specs will have no impact on this aspect of shifting behavior I'm afraid, though there is some contention that following the recommended fill only to 1/2 up the site glass will help shifting in general, just not the N to 1st clunk.
What you can expect is that the lower gears (1-2-3) do improve over time, which is quite likely a function of some wear, and perhaps more likely you get better at learning how to finesse it a bit, i.e. know its idiosyncrasies. At 18K miles now the bike (and me) shift beautifully, and that is even w/o using the clutch in the upper gears and I don't have Shift Assist Pro installed. Who knows though: it's conceivable that when the clutch and gearbox hit the 100K mile mark the clunk will diminish as those tight tolerances start to fade. But comparing brand new to 18K miles, no difference here.
I, for one, don't like the N to 1st gear clunk, though there appears to be no evidence that it harms anything. I tend to wonder if over the very long haul it may start to matter, but that is just pure conjecture. Because of N to 1st clunk I opt to keep the bike in 1st gear while stopped for shorter stops; for long traffic signals I kill the engine and leave the bike in 1st, after being mindful to be sure the traffic behind me is fully stopped. Because of this, I never experience this clunk. And as a side point, there bikes are only partially water-cooled and can get warm very fast in hot weather while stopped. So killing the motor in hot weather at a long light is a net plus IMO.
One other fine point. As you're coming to a full stop, downshifting from 2nd to 1st, I find it's helpful to shift briefly to neutral first, then with gentle pressure on the shifter she will fall silently into 1st gear as everything meshes up while you're slowing down. When slowing and not planning on stopping and dropping into 1st, it's helpful to not downshift until you're at or below around 18mph, and then you want to give the throttle more of a blip than you might guess, while giving a good 'definitive' shift into first. If you mambe pambe it you will confuse the dogs as they aren't sure what you're trying to do!
I would definitely give it some time on the 'jumping a little bit'. That really shouldn't be happening. Also, that is something that might be affected by overfilling oil, etc. Give it some time is my recommendation, and if it continues the clutch might need adjusting. My bike never did jump and I'm starting the bike while it's in 1st gear.
Fantastic bike, enjoy your new '16 ;o)