It seems pretty clear to me that in the case of favored souls, the idea was to create a character who's either good at offense, or good at defense, but not good at both. If you choose Cha as your higher stat, you get bonus spells, but your attack DCs are low, so you use your spells more for buffing and healing. If you choose Wis, your DCs are higher and you can nuke, but you get fewer spells per day.
For the most part, I see the favored soul, with his weapon focus and specialization, as an attempt to create a single-classed self-buffing warrior who can function as backup healer if need be.