I consider this to be very subjective, since it is the exact opposite to me. If a story is great, I can get over gameplay flaws out of anxiety to see what happens. I know there are other important things, like graphics, gameplay, scene connection and plot flow, etc. but I consider a strong story to be the very thing that keeps me on the edge of my seat. Plus, most Pokemon games have some standards when it comes to gameplay/graphics, so, since Reborn is equal/slightly above canon games of a certain Gen/era (which happened to be my favourite), I am more than OK.
Also, I agree 100% with you, the fact that the bar is being set higher and higher for fangames is incredibly important and Reborn has greatly contributed to it. We can have many hours of great chat about the flaws in Reborn and Rejuvenation too. And doing this is just a step in the process of eventually getting even better fangames! However, acknowledging what they have offered us is also important. And in my opinion, they are far better than any canon pokemon games.