The general HCB-F inputs are annoying with a controller, her HCL FRC stuff and FD cancel are much more comfortable/easier with a stick... Did you play C-Viper with a controller?
No, but I did practice her on pad a bit, since at the time, I was flip-flopping on whether or not I wanted to stick with stick, since the transition was so frustrating (I picked up Viper because I knew she was difficult and figured that would aid my stick training in the long run). IIRC, The only thing I couldn't accomplish with Viper on pad was naked, rapid fire TK cancels. At least, not without some finagling with macros. I wanted to stick with default, so I stuck with stick.
As for HC motions - I'm of the opposite inclination. I find them easier to do on pad. I almost gave up on stick completely because there was a time I
really wanted to play SSF4 Makoto (I was heavily influenced by Flash Metroid), but I couldn't do Kara-Kara on stick for the life of me. On pad, it's relatively easy. Stick is still inconsistent for me till this day, no matter what motion I use.
Maybe my thumbs are larger and flatter than others or something? I don't think I have large hands, though. I just find it strange that people struggle with motions on pad - I feel like I have to
try to miss inputs if I'm rolling my thumb along the directions, proper. Anytime I miss a corner input, I know it's because I didn't roll my thumb.