I'm reading through the cleric variants right now, and here's my general thoughts:
Losing Turn/Rebuke undead means no DMM and no way to get extra uses of Devotion feats without going into a prestige class that grants Turn/Rebuke. Rather annoying in my book, but thankfully other class features will mitigate this loss.
Loss of domains and their powers hurts. There are some excellent domains and powers out there (Planning or Trickery, for example). I rather enjoy the variety of options domains allow, but again it looks like class features mitigate this loss a bit.
Ancestral Speaker:
Extra skill points are nice.
Losing heavy armor is a minor inconvenience.
Ancestral Communion reminds me of a Factotum somewhat since it's a bonus to a certain skill. Unlike factotums, this can be applied to a no-ranks skill and it also adds the Charisma modifier. The bonus lasts for 1+Cha mod rounds, meaning that unlike a Factotum the AS can make several checks during that time with the bonus. I really like this feature.
Death Talker could be interesting, especially for an undead-heavy campaign.
Holy Presence obviates the need for a holy symbol/divine focus since the AS himself is one.
Improved Resurrection only saves a few XP here and there for the resurrected. I find there are better spells to bring back the dead.
Overall, it's pretty cool. Still T1.
Arcane Disciple:
Extra skill points speak for themselves. Losing heavy armor doesn't mean much.
Bonus feats as Wizard are very useful.
Arcane to Divine: Holy shit this is great. Every level the AD can learn a bard or sorc/wiz spell as a divine one, which means a lot of versatility and potential power. Magic Domain spells as regular spells are nice too.
Definitely T1, and a pretty powerful one at that.
Aspirant:
Extra skills like the others. Retains heavy armor use.
Spontaneous casting: Ability to drop any prepared spell and spontaneously cast any other is pretty powerful. It only goes up to 5 times per day at 16th level, but it's still quite a nice feature. Admittedly though, the ability to spontaneously cast once a day is about the same power level as a feat.
Shield of the Divine: Essentially a Monk's flat AC bonus going up to +5 at 20th level. It's somewhat helpful but still mediocre.
Divine Counterspell: Counter other Divine spells without losing a spell slot? Without knowing or caring what the spell is? That's a nice "screw you" option against the Aspirant's enemies. Ability to use it 3+Cha mod times per day is the standard "limiting" factor.
Perfect Self: As the Monk ability, IT'S A TRAP!
Middle or low T1.
Benevolent:
Extra skill points are always welcome.
Proficiency with all simple weapons, all armors, and all shields including tower shields. If you go strictly RAW, this variant is already proficient with exotic armors and shields, but obviously the intent is just what the Fighter starts off with.
Spontaneous buffs: Not just spontaneous Cure spells, a Benevolent can spontaneously cast all manner of buffs including Heal. Literally, holy crap!
Luck of the Gods: Bestow good fortune to someone which allows them to reroll any single die roll within the next 24 hours, as the granted power for the Luck Domain. Not only that, the recipient may add a luck bonus equal to the Benevolent's Charisma bonus to any single die roll during the 24 hours too. These effects can be used on the same roll. It can be used once per day at 4th level, and once more every 4th until it's 5/day at 20th. This power is bloody awesome!
This is what the Healer was meant to be. T1.
Crusader:
2x skill points, with minor skill tweaks. Not much worth noting.
Proficiencies will all armors and shields (including tower), all simple weapons, and with one martial weapon upon becoming a Crusader.
Deific Foe: At 1st, 5th, 10th, etc levels, designate a deity opposed to your own. You gain a +4 morale bonus on attack and damage rolls against worshipers of those deities. Depending on the campaign this might be useful.
Turn Foe's Followers: Turning undead is one thing. Turning and potentially destroying worshipers of the Deific Foe? Holy shit!
Bonus feats: At 3rd and every 5 levels after, gain a Fighter bonus feat, excluding (Greater) Weapon Specialization and including Combat Casting. Potentially quite useful.
Smite: Just like a Paladin, except the alignment restrictions on it working are only that the target doesn't worship the same deity and isn't the same alignment as either the deity or the Crusader. Not bad.
Definitely MAD, but still T1. The power to outright destroy some opponents leaves me agog at the possibilities.
Evangelist:
2x skills, add Gather Information. Not much really.
Losing heavy armor seems to be a theme with many of these variants.
Spellcasting: This puts an Evangelist into T2 because the class doesn't automatically know all Cleric spells. It's essentially Divine Sorcerer casting. However, the ability to spontaneously cast any domain spell puts the Evangelist high in T2. This variant meshes exceptionally well with Contemplative.