I would like Vincent and Yuffie to be made main characters. Have a forced encounter with Yuffie at some point, eventually leading to the Wutai side quest. Same for Vincent. Then have a brief line at the end like, "Vincent... Yuffie... get back to Midgar and get as many out of there as you can!" or something to explain their absence in the ending.

Or just have them in the ending and to hell with Dirge of Cerberus. I'd be okay with that, too.