According to an old issue of GameFan magazine (volume 4, issue 9), Alita was originally planned to be a playable character in Panzer Dragoon Zwei. From the magazine:
Sega’s animation division is currently working on an animated version of Panzer Dragoon that’s due out in Japanese rental stores later this summer. The storyline will be based on Panzer 1, but in addition to hero Kyle, will also feature Alita, a female dragon-rider that was originally going to be a selectable character in Panzer 2.
Jeremy Prusak has kindly provided a scans of the magazine:
I can imagine Panzer Dragoon Zwei’s story being quite different had Alita been a playable character. Perhaps she would have fused with the Guardian Dragon instead of the Dark Dragon or provided a further motive for Lundi to pursue Shelcoof. Or perhaps Alita was going to be the protagonist instead of Lundi.
I’ve also updated the Alita encyclopaedia entry, linking to one of the scans for reference.