I've got to agree that Second Edition did some cool stuff with religion-specific Priest classes that v.3.5--despite being far more flexible in every other respect--has sadly left behind. I don't see a lot of reason for every god's Clerics to cast cure or inflict spells, or to have anything to do with undead. I'd much prefer each domain to come along with its own spell list, completely replacing the standard Cleric list. I'd also like to see Clerics casting spontaneously, because praying at the beginning of the day to be able to use hold person three times and repel vermin once later in the day . . . man, that has never sounded
But, as long as I'm complaining, I've never really liked the whole idea of Clerics casting spells at all. Ideally, I'd rather see them lose the spells, and just receive a host of more powerful domain powers (which, obviously, would increase with class level), including effects like smiting, turning, and healing as part of appropriate domains. So the clerics of a life-related deity might heal and cure diease (Paladin style) and turn undead, while the clerics of some god of the forge might gain fire resistance, crafting skill bonuses, and Artificer-like item-enhancement powers.