I would say that making her short would seem like cutting corners in order to force her to be in the tale. It's what I'd expect to see in some other fan gaem. It would seem more professional and cohesive if she were either in it in her CT form or, if that is technologically impossible, to wholly remove her as a playable character. She would be interesting, of course, but I think one of the best things about this project is it seems to know its limits, and does things not for a 'coolness' factor, but rather on a more mature level (or, at least, that's what I've found so far, and what I can remember of, the story.) Even the very nature of its setting, between the games, rather than attempting to be a sequel, gives it in my eyes an element of class. You have nothing to attempt to outdo the extant games, no attempt to improve upon that which is there. AND you're sticking within Chrono canon. If Chrono Break is ever made, CE will not be wholly useless.
So, yeah, I think that things should continue as they've been going.