I would like to see a story that sort of tied up loose ends not just in one, but in both, so I picked a bit of both.
I could deal with new main characters, but I kind of like the idea of starting with Serge and/or Kid.
I'd like to see "Guile" replaced with MAGIL from RD, and I'd want the Trigger characters to not just make cameos but either be playable, or at least important to the story. Maybe Guile would just start to uncover his past, and roll with the amnesiac idea according to the Time's Eclipse ending of CTDS.
For example, I'd imagine Crono being a sort of like, difficult to unlock character to play, but he'd start out totally DECKED, as a symbol of his status as the original Lavos slayer. I wish I could draw, but it was along the lines of him wearing his Rainbow Specs kind of low on his nose sort of Jin-style (From samurai champloo). Instead of just wearing the sheath on his belt, he'd fight Iaito-style, like Vergil from Devil May Cry kinda, with his Dreamseeker katana. His lightning magic could possibly be replace with holy-style magic, or light-based? I don't really know.
If the main CT cast could be played, they'd need to be really strong.
I'd like to see elements get either redone or phased out... I liked magic better.
I'd like to NOT fight Lavos again as the final boss.