I think this is essentially the most desired system, especially by FF fans. I know of no other multi-player that has been able to effectively implement the system though.
That said, I think you're on the right track, but theres a few hurdles that need to be overcome.
First, the system needs to be either extremely limited to allow very significant combinations, or the system we currently have with many combinations with little to no unique combinations.
From my limited memory, I remember Chrono Trigger skills involving essentially two scenarios:
Combine some element with a basic tech skill, which basically turns into an elemental attack with a new animation.
Or
Team Up with one or more characters to use an entirely new skill unrelated to any specific attack.
From these two examples we have quite a few options. One benefit to this system is, there would be no need for any specific order to the attacks, and it is possibe for it to work within the current system. For example:
Player A Ques Blizzard > Player B Ques Skull Sunder II = *New Attack Brain Freeze* ( Random name)
If you change the order, the result is the same. A new attack that requires both players acting simultaneously.
The second Scenario is a little trickier however, as you would need some mechanism by which new attacks are selected under certain circumstances. One idea that pops off the top of my head, is to add an action to each class called "Cooperative Tactics" when selected would bring up a menu. The menu would include all available techniques that can be performed with the classes in your party.
For example:
Player A & Player B have a combined 4,500 TP, both of them can select the cooperative tactics action, and select the ability. Once selected the two players begin the new technique.
While either would be certainly more interesting, they would involve alot of work; and we wouldn't see any results for a very long time most likely. Personally, after having played with the current system alot, it does leave alot to be desired, but I have enjoyed it so far.