It seems Freespace has gone through plenty of changes since I have been away. These new lens flares look great, and I thank you for posting the updated images Admiral Nelson. While I do agree that the lens flares blend in very well with the new stars, I also agree with Admiral Nelson that the lens flares' similarity in color and configuration obscure each star systems' individuality.
To improve color, the halo and the two horizontal "rays" should have a hue that is similar to that of the star. I do not know if it is as easy as making the lens flare's RGB equal to that of the star, but it could be worth a try (assuming that is possible). Nevertheless, adding variations in color will be a necessity.
To improve luminosity, the only solution that I could think of is to experiment by increasing or decreasing the size of each lens flare or star in a particular system. Before, I would always add a lengthy description of each star system, discussing subjects like apparent magnitudes, separations of stellar components, and luminosities in solar units. I now realize that dealing with those exact values is not an easy thing to translate onto a computer screen. For example, if I were to say that Sirius A and B have luminosities equal to approximately 25 and 0.025 times that of the Sun, how would we handle those values in a Freespace scene? One way to deal with these quantities is to approximate each case relatively by adjusting the size of the stars and/or lens flares.
It was a vision of mine from long ago to see the day that Freespace had stars which looked similar to those from Freelancer. While not all of the stars in Freelancer are dissimilar, the different numbers and formations of rays added to the variation. Currently, I have no problem with the two horizontal rays, but if it is possible, changing the size, number, and position of those rays might help to lessen the obscurity mentioned earlier. I don't know if this is possible at the moment, but if it is, we will have the options we need to create more unique scenery.
That's about it. What I can do is use Celestia to help establish some sort of template or guide for you to follow, Admiral Nelson. I will use your screenshots to help guide me along the way, just like I did with Sirius, so you won't have to worry about repositioning the primary stars. So with Sirius A's apparent diameter set as a constant, the size of the lens flare halo will give you an idea of how large the lens flare should be. Then, the radius of Sirius B and its lens flare could be adjusted to match the Celestia image. How does that sound?