I haven't read completely through all 13 pages of this thread, BUT I think the most simple solution would just be increasing the effectiveness of SC.
Basically:
Keep - all the setups, combinations, skillchains, the magic bursts, and even the timings the same. (Although a little more leeway on timing would be nice, even a second for laggers).
But simply change the damage of skillchains or the damage bonus of magic bursts and maybe reduce the enemy's stats.
Imagine a simple Scission, an earth elemental based effect, which lowers the opponents Dexterity, which is commonly associated with the lightning element.
Now imagine Dark/Light skillchains. Which would lower more of the enemy's stats.
Now that is just weapon skills. Physical Damage - Physical Stats reduced.
Next step would be Magic Bursts.
Let's say the first Scission is MB'd with a Stone 1. This should increase the enemy's damage cap taken against Lightning based attacks.
This would lead to another round of Skillchaining and Magic Bursting. The team would need to rotate weaponskills to create a SC to take advantage of the new Lightning weakness.
Of course this is still a lot of planning and understanding of mechanics, but it would definitely be worthwhile against harder enemies and missions.
So maybe update the cap of damage of skillchains. Example: level 1: 100%, level 2:200%, level 3:300%
Although this may seem like a drastic increase, how often do you ever see a skillchain involving more than 2/3 weapon skills?
2 Members spam Weaponskills for maximizing their own damage...
OR
2 Members spending the extra 30 seconds for each other and coordinating a proper and VERY effective skillchain to maximize the overall damage.
From what I've seen the 30 seconds is too much for just a 100% bonus damage SC, when they could just burn the TP and do another WS for just the same amount.
This is why increasing the damage and creating an alluring incentive for people where they can see the significance of teamwork.