I will address some of your points and allow others to hit the rest...
Some R9 critics view this "design decision" a bit suspiciously. Who? What is "suspicious" about it? Some conspiracy to make bullets tumble?
The R9 already suffers from many critiques like "custom" price tag,Its more of a "semi-custom" price for a semi-custom gun.
extreme waiting time, Something Rohrbaugh has taken extreme measures to address, but it happens to lots of things early in their product life if they are much anticipated and somewhat revolutionary -- Mazda Miatas, PT Cruisers, Nintendo 64s, etc.
inability to shoot +P ammo, A design choice necessary to fullfil the mission of the smallest possible 9mm autoloader.
European style mag release,A design choice -- the heel release was believed to be better for a pocket gun and less likely to be inadvertantly released. Given that this is not a speed-load type gun... it was deemed the best choice.
lack of slide lock,A design decision to make the gun as simple, reliable and thin as possible.
lack of nightsights,Lack of nightsights! Heck, the designers had to have thier arms twisted to put sights on the gun. They have no idea why you would want night sights on this gun!
and so on. Each of these can be discussed and evaluated logically, Yep. Guess I just did. It has nothing to do with logic -- just and understanding of what this gun was designed to do.
but the tendency not to plant a bullet squarely in a target is a bit hard to "defend". I am not sure I agree with your characterization of the gun's performance. Nor am I sure that it completely matters unless you are relying upon your hollow points expanding to get the job done. I am no ballistics expert and I will let others address these issues.
Is there a "plan" by the design team to address this at some point in the future?Don't know. If it will require the elimination of the free bore, it isn't possible without making a gun larger --- which would make it a different gun.