I don't currently have anyone in my game playing a cleric (out of six players -- believe it or not), so perhaps this is moot coming from me...
As to access to certain spells, well, there's no reason you can't change the level at which gods grant certain spells to certan clerics: a war god may grant healing, but cure light wounds is as hard to channel for his cleric as, say, magic vestment -- for that god, both of these spells are 3rd-level... Further, you can always max out the spells granted, so that such a cleric will never get anything more than cure serious wounds, which might be a 6th-level spell for his clerics.
Further, I think that if you want to individualize gods' spheres more, you need to design carefully the full list of available spells for each god -- arbitrary lists of "domains" are still too wooden, I think, no matter how much you tinker. Why should a god of crafting, with incidental access to fire spells, get the same fire spells as a cleric of the god of fire and destruction??
The spell lists should be much smaller, too, I believe. However, I don't have a problem with taking some of the spells from other class lists (even arcane spells) if they suit the god. Generally, to balance the loss of spells, I'd give granted abilities specific to the god as the cleric increases in levels (these generally copy and/or replace domain granted powers, but take them somewhat further, as well). I'll give an example of what I mean below.
Also, I have made spontaneous casting apply to a tight group of spells closely associated with the god's spheres: for instance, a cleric of a fire/destruction type god would be able to cast a couple spells from each level spontaneously, but not cure spells: rather, fire and destruction ones, so he'd never need to prepare those spells.
Here's an example -- spells granted to clerics of the neutral-aligned dwarven god Dumathoin ("Keeper of Secrets Under the Mountain") from the GH setting:
Powers granted at given levels (I didn't try to copy the table over here, because the formatting always gets screwed up):
1) rebuke or command earth elementals as an evil cleric turns undead, spontaneous casting
2) generate protective ward 1/day (as Protection domain ability)
4) nondetection 1/day
6) +1 resistance bonus to all saves vs magic
9) gain Craft Magic ARms and Armor or Craft Wondrous Item
11) need not concentrate to control conjured earth elementals
13) affect / influence earth elementals as if wearing a ring of (earth) elemental command
Spells Available
(note that many of these are home-brewed or converted from various 1st and 2nd ed. sources, or else from the WotC splatbooks or S&S's Relics and Rituals)
*Indicates a spell that can be cast spontaneously.
0-Level: Clean, create water, detect magic, guidance, mending, purify food and drink, repair minor damage, resistance*, shockwave*, spark, virtue.
1st-Level: Alarm*, bless, detect gold*, detect secret doors, endure elements (fire), hold portal, identify, magic stone, magic weapon, nystul's undetectable aura, protection from chaos/law, repair light damage, shield of faith, shockwave strike, silent image, smelting.
2nd-Level: Aid, blindness/deafness, delay poison, endurance, heat metal, magic mouth, make whole, misdirection, obscure object*, repair moderate damage, silence, soften earth and stone*, spiritual weapon, strengthen structure, zone of truth.
3rd-Level: Arcane lock, continual flame, create food and water, displacement, find traps, glyph of warding, greater magic weapon, illusory script, ironheart, magic vestment, meld into stone*, repair serious damage, resist elements (fire), sacred weapon, stone shape*, summon nature's ally III (earth elemental).
4th-Level: Detect scrying*, dig, dimensional anchor, discern lies, dispel magic, divination, ghostdweomer, hallucinatory terrain*, ignite metal, illusory wall, modify memory, repair critical damage, seal of Hedrada (called "seal of earth"), spell immunity, spike stones, unfailing endurance, wall of earth, weapon of the deity.
5th-Level: Commune with nature (outdoor range, but only usable underground), hatch the stone from the egg, false vision, fire shield, mirage arcana*, Mordenkainen's private sanctum (called "Dumathoin's private sanctum"), neutralize poison, passwall, repel metal or stone*, summon nature's ally V (earth elemental), transmute mud to rock/rock to mud, true seeing, wall of stone.
6th-Level: Animate objects (stone or metal), forbiddance*, greater glyph of warding, move earth, reverse illusion, statue, stoneskin, stone tell*, summon nature's ally VI (earth elemental), wall of iron, word of recall.
7th-Level: Animate rock, blade barrier, earthquake*, refuge, repulsion, transmute metal to wood/wood to metal, summon nature's ally VII (earth elemental)*, symbol.
8th-Level: Antipathy, dimensional lock, iron body, legend lore*, protection from spells, screen*, summon nature's ally VIII (earth elemental).
9th-Level: Elemental aura (earth)*, elemental swarm (earth), glorious transmutation, miracle, summon nature's ally IX (earth elemental)*.