It’s good that you have SWG-0027 in the Vader role. Regarding her, you could have her replace the Jedi clone that fights Anakin and Obi-Wan at the beginning (that way the two sides can have some familiarity with one another), which could end in Clonemaster Jukassa’s death by the Jedi’s hand (or by hers?).

Another idea (and this is just throwing it out there) is that she wants to overthrow the Clonemasters and establish a superpowers for clones and ONLY clones. This could make her interactions with her second-in-command more interested, as he was constantly jabbing at SWG. Maybe he was really loyal to the Clonemasters only and suspected SWG of treason, which is hinted at as SWG gathers clones (loyal to her) on the battlemoon, at an attempt to use it on the Clonemasters.