I had this same issue, and I just discovered a really easy fix!
Mark is right that the issue is subpixel rendering. The AE lens flare doesn’t use it. None of the issues Dave mentioned are relevant in this case, but I do appreciate his taking the time to try to help.
THE FIX: Make AE subpixel render it.
Go to the solid settings and resize the solid. I multiplied it by x3–not perfect, but much improved.
Then, fit the solid to the comp size (reducing its size by the same factor). Voila, a smooth, subpixel-rendered lens flare.
This works even when you use a 3D Null to drive the flare center point (which is what I’m usually doing). The only caveat is you have to multiply your toComp expression by the same size factor to produce the right result. For example (on the Flare Center property): thisComp.layer(“Sun”).toComp([0,0,0])*3