The cleric is way overpowered, but my main problem with domains is that they raped the sorcerer/wizard spell list to fill them up with high-level spells.
Here's what I would be inclined to do to "fix" clerics:
* Either make spell failure apply to clerics, or remove it from arcane casters. A gesture is a gesture, after all, and a spell with somatic components requires "one arm able to gesture freely". Do we really think that the gods are watching over the cleric's shoulder, and if they screw up a gesture slightly due to their full plate mail, the god goes "Oh, that's OK. I know what he meant!" Sheesh. You're not going to see wizards running around in armor all the time anyway--they would need to invest a good stat in strength to wear anything better than the Mage Armor spell, and spend feats to learn armor use. If they get around these restrictions by multiclassing, they're losing out anyway by falling behind in the spell levels.
* Fix some of the domains to better reflect their theme, inventing new spells if necessary with a more priestly feel to replace the wizard spells. A warpriest, for example, should have spells which affect large numbers of troops at high level--not power words.
* Associate each deity with one or more Divine Mandates that restrict the character's role-playing options. After all, that's the supposed justification for clerics being overpowered--that they're not free agents. The "dogma" sections of Faiths and Pantheons are just watered-down philosophies, not at all restrictive. What are the deity's goals? The cleric should be pursuing them night and day.
OK, that was a nice little rant. I feel better now!

Now that that's off my chest, the ideas being bandied about here are all very good. I especially like the idea of replacing "Turn Undead" with other appropriate powers for each domain. A lot of them (alignment and elemental domains) will still be turning/commanding based, but I'd like to see the cool alternatives posted here.
--Ben