I don't think any key Square employee went back to Nintendo after FFVII. As a matter of fact they hardly had any relation with them for two entire generations.
You're forgetting the folks at AlphaDream. Before forming that company, most of them were Squaresoft employees, drawn primarily from the Mario RPG team. I believe Brownie Brown folks were also drawn primarily from Squaresoft (Secret of Mana), although I'm less sure about that.
The fall in the reading comprehension in this community is worse, SE Japan discussed all over, when they have nothing to do with the subject matter.