I think they're trying to combat the issue that not every job can compliment each other when double stacked.

Barb + Bard = Easier silence / more songs
Black Mage + Black Mage = Massive AoE / Burst Damage

Other classes when stacked together don't give such a strong advantage. (Enlighten me if they do)
Now there's a choice to make. If you want to double stack classes then your limit break charges slower.
Pros and cons for everything!