team based abilities like something from chrono trigger would be neat to say but I'd imagine hard to implement. I get what you are trying to go for with the concept and I can see it working, it would lead to a lot of interesting variables if implemented properly. Perhaps as a balanced, well there's 2 ways to go about it. The mastery is only effective under that subjob or you have to set your masteries just like blu spells. So you can't basically have a BLM master all their mastery skills with each sub job, it sounds a tad to powerful lol.
With weaponskills though I can see something like x readies ws, and then they wait for y to ready weaponskill and then they go, but there would be an option to cancel the ready if other player wasn't ready. Though I do imagine there may be a lot of animation issues if something like that came into effect.
Speaking of team based abilities I've always thought that perhaps "Meteor" should be a two blm spell, since it is a pretty overpowering spell. or heck if not that, depending on it's potency they could do two things.
If you cast Meteor by yourself it takes 45 seconds.
-Cost half of max MP
-recast is 5 minutes to recharge your fatigue from casting the spell
If you ready Dual Cast on target you stand still and once other BLM uses Meteor it'll automatically put you in casting animation
-spell will fail if the one using "dual cast" moves
-Spell saps 400 MP from both users
-recast is only 1 min
-casting time is 15 seconds
That's the best I can think of in an example of "dual magic" having a JA that readies it may work.
The same can be said for Weaponskills. Perhaps there can be a "ready command" for a team based weaponskill that last 1 min or until target uses weaponskill. Basically you use the ready command on the Ninja. Then the Ninja uses weaponskill "Blindside" While the weaponskill is being readied it checks to see if the one that "readied" the weaponskill has TP and access to using the weaponskill and if show the weaponskill takes effect.
But ya overall it would be neat to see some teambased abilities just for the sake that unison attacks do look cool. It would open a nice window for more unique abilities to be added that varies based on setup.