I'm not sure. From memory, in Netossa's follow-up appearances, she mainly just served as a damsel in distress. As such, perhaps they chose to use one of the few named members of the rebellion who didn't have any super powers to make her capture more reasonable? Of course, that still doesn't really explain where Spinnerella was.
Maybe Spinnerella died in battle in a "lost episode" and in dedication to her memory, Netossa continued fighting with the rebellion, but her heart just wasn't in it so she wasn't quite an effective warrior? Maybe Spinnerella and Netossa learned that the Horde had invaded their region of Etheria and Spinnerella left the Whispering Woods to help protect their homeland, but Netossa remain to help the rebellion? Or maybe Spinnerella journey to Eternia to elope with Sy-Klone and make cyclones together?