I believe you should only take absorbance within the linear range for standardization, which is between 0.1 and 1. When absorbance is below or above the linear range, it no longer correspond to the concentration correctly. So your smaller graph is correct. In the same manner, measurements that you make need to be within the linear range for it to be a valid measurement.
I had submitted the graph for publication, they commented on it saying not to connect the points since it is not an xy plot. I am confused, the plots or graphs should be connected to show the linearity, if it is not how can we express the linearity?
ELISA are following the Rodbard-Function. That's a 3 or 4-parameter exponential function. In most ELISA readers this function is included. Alternatively you can use a spline approximation.