I agree with you two-player mode would have been a mess because of the combination techniques alone. But to play the devil's advocate, I can also imagine how fun it would be if a player and his or her friend were playing the game they knew by heart and worked together and learned to work a system out between each other to co-operate. In the same room with little lag, instead of these kids and their blasted Internet, it would be an exercise in frustration until synchrony ("SynChrono Trigger") is achieved, making the combo techs very meta.
There are other solutions to the "you stole my turn" problem, one of which is to require combo techs to require the consent of both players. For instance, the first player selects it and the second player confirms it (assuming he or she controlls both characters), and if the second player denies it and a character whose ATB bar is filled, they can select actions from their own list. Yes, there is still a "wasted time" issue due to only having one selectable menu onscreen at a time and there are much more elegant solutions to the problem that has been created with opening up the Pandora's Box of a two-player co-op.
Concerning the idea of more playable characters in a party by itself, while the number of unique-palleted and animated characters (so many tiles) in Chrono Trigger wouldn't the battle system itself also cause problems? As much as I love FFVI, the battlefield itself is static despite the deeper customization of the playable characters. By contrast, Chrono Trigger deals with enemy positioning and AoE attacks aside from the animation/sprite composition, and adding an extra figure on screen would complicate matters. Would it even have been doable within SNES limits and if so, if everything was pared down to a lesser complexity, how much would it still be Chrono Trigger?
Still, if in a magical world where it could have been done without sacrificing the aesthetic, I was imagining what it would be like, and was wondering what anyone else would have thought it would be like. Just radically daydreaming...