The whole Cir-El thing depressed me, really. I don't know whether they had just the one long story-arc in mind for her that ended with her being an altered human and a pawn for Brainiac, but it seems that, like Linda Danvers, she got the short straw because she wasn't a classic version of Supergirl.
The odd thing is, Loeb uses her fairly prominently in his run of Superman/Batman, but then is instrumental in bringing back the so-called 'true' Supergirl, which makes me wonder if it was something like an editorial decision or something he proposed and Didio used it as part of kicking off his silver-age revival.
Regardless, it's nice to see someone else has appreciation for the character. I've only known her through the Superman/Batman trade of Public Enemies, to be honest, but she certainly seemed more interesting than Kara.