Project Idea

As someone who has had this idea (to the point of coming up with Double and Triple Techs for some FF6 characters), my blunt advice will be to not even attempt to do this with romhacking.

While Chrono Trigger and Final Fantasy VI have a lot of similarities in terms of being Square JRPGs, structurally, both games are vastly different. It's not as "simple" as crossing over two platformers (like Mario and Mega Man, for instance). Looking at the bare basics, both games utilize different environment and sprite construction, different battle schemes, different party limitations, and so forth. You would essentially have to convert one game to the other...and you'd lose everything that made each game great.

If you were to convert CT to FF6 for instance and hack FF6 (and this is the only remotely feasible direction), you would have to have the Chrono Trigger cast use the Final Fantasy 6 system. All of the wonderfully animated sprites would be lost and replaced by Final Fantasy 6 style replacements. The whole offensive arsenal of Final Fantasy VI would have to be severely limited to approximate CT's approach, and battles would be rendered boring since enemy position and combo techs would be useless even if you could implement them. We're not even getting into things like the 999 vs 9999 HP limits, the differences between statuses of the games, the tile and pallete re-writes, and of course, recreating all of the endings and implementing a NG +.

And if, somehow you were going to convert FF6 to CT (which is what I and probably every SNES era fan would prefer), aside from the fact that you would have to re-sprite every single character, tile, background, and give even mundane enemies animation, there are some hard limits, such as CT having 3 characters in a party that you cannot overcome. Because of that alone you will have to rewrite the story to follow the gameplay. That's not counting the different element system, the difference in character equipment, and so many other things. You would have to redo Final Fantasy 6 entirely to make it fit into CT's style...and that's just on pure concept. Let's not get into SNES limits for VRAM and such.

If you want to make a crossover like this, you're either going to have to wait for the FF6 SDK to get finished or put a fire under some CT fans to make a CT engine that is flexible enough to allow for a FF6 remake to be done with it (meaning they'd have to plan for this possibility from the get-go and allow for an expanded element system/status effects, four characters, two accessory slots + a shield, Espers and spells learned from equipment). Even then you would need help from lots of different spriters to essentially sprite a new game.

Believe me, I would LOVE for something like that to happen, but this would have to be done with a new engine (and no, not RPG Maker...I mean coding from scratch), not a romhack