A view is rare if it is not one of the over-represented ones from your 2D. Could also utilize this: Orientation Sorting Tools - #7 by robertstass?
From your 2D/3D above, the view that is most represented (at least in 3D alignment) is looking at the triangle. your “side” and “top” would look better if more particles contributed there. so in your 2d just take class 1,3,4,(maybe 5 seems most rare)7,8,(9 also very rare “top”) etc, and disregard 2,6,10.
Strangely, from the 2D above you have great distribution. So it could be a problem that your reference is anisotropic and therefore your particles fit best to the preferred view, exacerbating the effect. Or more likely, the 2D you showed is not the same particle set that yields the 3D shown.
If you take those 2D shown and run ab initio 1 class, 2 classes, 3 classes etc and look for any single good reference, I would expect that NU-refine (or het refine of multiple copies) of all particles in the shown 2d set would look great.
as for topaz - no need to re-extract pristine particles. it doesn’t “see” the 2D classes, it “sees” the particles which includes the background noise of near particles.