Maybe this should be house rules, but...
I think a spontaneous caster makes more sense than prepare spells, but thought Favored Soul's biggest drawback was the lack of domains. Domains are the best part of the 3e cleric class, and Favored Souls lacks access to domains.
Instead of having a spells known per level chart as the sorceror class, I would just have granted the Favored Soul all of the domains of his or her deity. Then only domain spells could be cast by the Favored Soul. I would have dropped some of the class abilities in exchange for the various domain powers.
Result: A class much more specialized towards the Deity.
I would also allow the Favored Soul access to the various Initiate feats and the various PRCs dedicated to a specific deity.