Changing Guile's character model texture to more resemble Magus should be very doable (blue hair and eyes would be a quick job with proper color replacement), in addition to giving Guile Lynx's scythe (some pointers would have to be changed, perhaps, if the weapon models are very different in size). It could be the first non-translation Chrono Cross patch.
What I'm not quite sure about at this point are storyline changes and model animation changes. Terminus Traductions has unraveled the compression for the game text already, enabling us to change Guile's dialogue if we wish, but I haven't the foggiest idea how we'd go about scenario editing like Temporal Flux allows us to do with Trigger. Changing character animations (for example, getting Guile to hold a scythe like Lynx) will be extremely challenging, and might need to involve bone rearrangement at the hexadecimal level.