Ind + Phi could be toned down "behind the scenes" so-to-say:
If there are modifiers on the random generation of the location of Stone and Marble vesus your starting location - and I do not know if there already are factors built in to the game to account for traits and UUs and UBs - then maybe a larger modifier could be coded in for this trait. That way anytime the Ind + Phi combo was played Stone
and Marble
and Gold could be coded to be almost always far, far away - based on difficulty level of course.
Secondly, the random game could preferentially choose some strong Industrial AI leaders so that getting The Pyramids would be very competitive and next to impossible at higher difficulty levels.
Those are two ways Ind + Phi could be toned down without doing anything obviously over-compensating/correcting. That way the Ind + Phi led civ would be challenged to get things a going - it will still be a strong trait, but at least it will be more likely delayed before it "takes off"!

One would hope!
Back to OP...
My suggestions on the 3 traits:
Charismatic/Creative - a leader for Spain, Isabella's husband Ferdinand? They were in fact a team, so it may work very well conceptually speaking. Play one or the other and, in a team game,
both could be in play!
Organized/Protective - a leader for Japan: Emperor Meiji fits really well! Meiji played a profound role in Japan's rapid change from a feudal society to a modern industrial one. I think many civver's would like such a leader in the game.
Industrious/Philosophical - a leader for... oh this is tough... hmm... the Celts have two aleady... the Native Americans. Because they are such a large diverse group of peoples... How about young Chief Pacaha who led one of the more powerful Mississippian tribes of the 1540's (as per Spanish accounts)? The Mississippian tribes were on their way to really building cities (they built large mounds - some almost pyramid-like) but died out before they had a chance to flourish. Other than Pacaha there is Geronimo and Hiawatha... But Hiawatha was spiritual and Geronimo was aggressive, neither particularly industrious

I don't know who else but Pacaha for a 2nd NA leader given this last trait combo.
Of course juggling trait combos around opens possibilities! (I'll let others do that

)