Vega SSFIIX uses Mugen 1.0 SFF v2 format, allowing for more than 12 colors to select from.
Vega SFII'CE uses old SFF v1 format. Only 6 colors are available for this file, limiting to only his 3 original SFII colors.
You can change the current palette in game by pressinng Start before the round begins, this brings up the color select menu.
Change the colors by pressing left or right. Pressing up or down changes between SF2-X version, or the SF2'CE version of Vega.