Unlike most Cross-haters, I don’t mind the fact that CC is different from CT. In fact, I salute the designers for taking such a bold step. My dislike stems from many of these changes resulting in a game that's less fun at best and painful at worst.
But how to fix it? There's the real question.
First, ax the following characters utterly: Pip, Orlah, Pierre, Doc, Leah, (her alleged connection to Kino and Ayla is irrelevant to the story, and obviously thrown in as an afterthought homage to the two CT characters), Van, Mel, Irenes (her I could see as an NPC) Funguy, Skelly (again, make this one an NPC. The collect-the-bones bit could make a fun side-quest with a neat reward, though), Greco, Neofio, Turnip, Mojo, Draggy, Janice, Macha, Orcha, and Korcha.
With that dead weight out of the way, we are free to enhance the stories for Lenna, Norris, Nikki, Luccia, Razzly, Zappa, Miki, Starky (perhaps the character with the single greatest wasted potential in the entire game, story-wise) Sprigg, and Steena. Especially Steena.
Keep the element system, and the battle mechanics. Only enable the use of techs more than once per battle. I mean, really, what kind of crap is that? If you're worried that might make battles to easy I guess you need to work on monster difficulty a little bit more, huh, Square? And there should be a definite advantage to an innate element color when it cones to using elements. I know the game says there is, but i could never tell any difference.
And a decent ending would be sweet. Staring at a text window and blurry image of a planet while Schala/Kid rambles on and on is boring and resolves nothing of the gorram plot. Yes, its all very deep and meaningful, which only makes seem more out of place when the rest of plot the game pretty much equates to "a wizard did it".