Additional uses of rage don't make the barbarian more powerful at all. It just gives them more chances to do it throughout the day. Especially in the case of rage, where it's explicitly limited to once per encounter, it just means that the player is going to get to do the thing that makes his character cool in more encounters. If he could have chosen to rage in encounter A, or he could have chosen to rage in encounter B, but not can rage in both A and B, you haven't actually increased his potential power in either encounter.
I mean, I can certainly see your viewpoint that allowing him to rage in both encounters is kind of like allowing him to bypass a "penalty" of not being able to rage. I just don't think it's a huge deal.
So how about the following changes:
*Cleric: Additional turn/rebuke attempt each day.
Not really sure about this one... It fits the theme a lot better, but at the same time I think I really prefer my other one (adding wis to turning checks in addition to charisma). I like that it makes the checks more potent, rather than just letting you make more.
*Druid: When shapeshifted, the druid's natural armor improvement is increased by 50% or her wisdom modifier, whichever is lower. For example, a level 16 druid with 22 (+6) wisdom in ferocious slayer form has her natural armor improved by +12 rather than +8, while the same druid in elemental fury form would gain an improvement to natural armor of +22, rather than +16.
I've pretty much decided now that I'm going to make Shapeshift standard for druids in my campaign, and get rid of wild shape entirely.
*Monk: For all purposes EXCEPT base attack bonus and base saves, the character is treated as if his monk level were one higher. Note that this means the Flurry of Blows table will not be correct for your character, as you'll gain additional flurry of blow benefits sooner than you would normally. At 10th monk level, the monk is gains abilities of a monk two levels higher.
I don't think any of the monk abilities are especially unbalanced if you get them earlier. Unfortunately, stunning fist is a bonus feat which they can choose not to take, meaning I can't just give them an extra use of that or something.
*Ranger: Gain an additional favored enemy at 1st level. Both 1st level favored enemies start at +2, and increase as normal when you gain further favored enemies.
I like this because, frankly, I absolutely hate favored enemy, both as a player and as a DM. I don't like it as a player because I have no idea what the DM's going to run, and I don't like it as a DM because I'd feel like I'm screwing over my players if I don't run them against their favored enemies. At least with this option, they get more favored enemies, opening up more opportunities.