Also, I'm comparing it to the base healer, which is a pretty weak class, but has 100% spontaneity. While I like the direction you went with giving prepared spells, and a smaller selection of spontaneous spells, I find it funny to imagine a Healer who can't actually spontaneously cast healing spells, while any cleric who's CoDzillaing it up without actually caring about healing can. Giving the cure domain as the first domain 100% of the time, or making it a bonus domain in addition to the others.
The rest of what I mentioned falls under the realm of "would be nice". The advanced learning spells becoming spontaneous would translate into 5 extra spontaneous spells known, and chances are those spells won't be affected by the majority of your class features.
Honestly, I'm not sure. I just know when I looked through the domains and saw more than half with the same 9th level spell, something seemed off. I mean, someone could avoid that problem by taking deity domains instead of the overlapping domains, but it still seems... wasteful. There may be something in spell compendium, or really even make something up that is fitting with the domains in question, since you're already homebrewing.What other 9th level domain spells would you suggest?