Simplifying and giving many options are somewhat mutually exclusive. The current domain rules are somewhat complex. You can create tons of various with the combination of domains (and feats and such). Also, each domains are not equally powerful. Thus, I do not recommend to use the existing D&D 3.5e domains as they are.
Well, If I were you, I will only use either Domain granted powers or Domain spells. And in either way, I will re-arrange, simplify, and try to make each domains equally powerful.
If I choose the former, I will make each Domain powers as simple as possible. Say, a +1 bonus to something and such.
If I choose the latter. I will likely to make 2-4 or so of domains which I like, make domain spell lists, and simply make those spells available only to a cleric of certain domain. A cleric should have only 1 domain. And If I were you I will get rid of domain spell slot rule for make it simple.
Also, making Wizard and Cleric as spontaneous casters like Sorcerer will be good for simplifying the rules. It will also make the game faster.
My idea at the moment is for a clerics to have close to 20 spells in general then gain 4-5 more spells from their domain (clerics only get one domain). The domain bonuses are pretty sparse too like the War domain allows the cleric to make a smite attack in place of one of their turn undead attempts and gives proficiency with the deities favorite weapon.
I am tweaking the spells to all be somewhat on the same level. What with their being only 1 power level for all spells that I have. And yeah I their is no domain spell slot the cleric just gains access to their domain spells.
No real need to make either cleric or wizard spontaneous really they both have relatively few spell slots. A basic cleric only has 2 while the mage has 3, though their are class abilities to increase this these slots do not increase with level. You have to buy them with your class ability.