well its your mod, you can choose what you please with the SP thing, just think how bad FF8's draw system is for stat building hehe.
but overall I think it would be best if everyone got equal SP, i don't see how it could work any other way as how would you scale things back for certain playthroughs with different party members.
not sure at what points you mean when talking to them in the story, i guess your basically asking the player which one to increase its stats, sortof like a choice, im not sure if that's such a good idea either as then the player would feel forced to keep whichever one he chose in that situation, and for the choices where the player can't choose to talk to a certain party member , he wont get to use them, but its your choice at the end.
its most likely the player will be doing everyones new threat boss anyway to get the party read to take on the final story bosses, you can give SP points for that particular character for each of the boss fights, but its most likely you will expect the player to do all of them anyway, so it wouldn't much either way.
yeah half the new threats bosses are really cool, but i hope barrets and cids get replaced with something better, i never got to see tifas.
what is with this new boss towards the end of this video
I don't remember encountering it in 1.2.
Also I would suggest blocking off the final story bosses until the new threats are taken care of, including the weapons, and then you will be strong enough to do the final story bosses.