Warrior Toughness
O.K., here are my thoughts.
It would be easier to judge balance if I knew all the other classes you would be using. Assuming that you are using classes like those in AU, I think the champion will be weak compared with this class (without some tweaking). I took a look at your 'campaign site' through the link in your sig, and I would really worry about a berserker type class alongside this one. With the warrior's ability to rage, why would anyone bother.
As to the specifics of the class, here are my thoughts.
If you are fine with letting everyone have more skill points, the increased (4/lvl) skill points are fine. Keep in mind that this fairly dramatically opens the skill options for a warrior class, as there are many ways to easily add another two or three class skills using warrior abilities as listed. I am fine with this; I do it in my own campaigns, and no problems so far.
However, I disagree with the ability to trade skill points for maximum hit points (or a higher hit die). If you are giving more skill points, then the assumption should be that they will be used on skills, not directly affecting the character's ability to take damage. I would keep these separate, for the same reason that I would not allow players to use their characters' skill points to buy more spell slots, or new spells known, or more sneak attack, or a feat, yada yada. It just messes with the balance too much; skills are meant to be relatively independent of combat balance (they aren't, but letting them influence combat more doesn't help).
So, with all respect, I don't like the idea. It is made worse with four skill points per level, and it lessens the impact of the resilient warrior's HD benefit. If you are absolutely wedded to the idea of allowing warriors this option, then keep the costs the same, and reduce the skill points to two per level. But really, I think you should jettison the idea altogether.
I like the warrior abilities, for the most part, and the number of feats and abilities is really more like what it should be for the fighter, in my opinion. My comment about rage applies only if you have another class that does the same thing, like a berserker/barbarian. Unless the berserker can use the ability far better than the warrior, there will be little point in making a berserker.
Do you have a ranged fighting class? As it is, the warrior could cover the bases, but there really aren't any warrior abilities specifically suited to archery, or a thrown weapon style. Usually, an archer would become an agile warrior in your system, but it feels like fitting a square peg into a round hole.
I think that the inner strength ability is too powerful and too weak for the agile warrior. The first time you take it, it gives you a temporary two point bonus to dexterity, and the equivalent of rapid shot for a melee fighter. As early as you can get this, it is probably too good. Why use two weapons, one of which will do less damage and apply half your strength bonus, when you could use one with this ability and get more out of it? That is probably a problem with two weapon fighting, but there you go.
The second time you might take the ability, it is far too weak; this time, it gives: an additional +2 to dexterity. If you are a ranged fighter, or using weapon finesse, this is a +1 to attacks and a +1 to AC. Not so hot. If I were designing this ability, I would probably give the character the ability as written the first time, but with a -4 penalty to all attacks instead of +2. The second time, it should give the total +4 to dex, and make the penalties -2 instead of -4. And you should get an additional use per day of the ability when you take it the second time, for both types of warrior, I think. It might even be worth it to allow them to take it again for increased benefit; a warrior could be built on this style.
I think that weapon mastery is a good idea, but considering the costs required, it should be better than it is. Or, at least, not so weird. I think the increased threat range is a good idea. I think that the second part of the ability is a mistake; letting warriors use their increased threat range to make it easier to hit creatures that they otherwise would have missed just complicates attack rolling, and why should the ability kick in at all for warriors attacking creatures they could only hit on a natural 20?
I don't have any good suggestions for a replacement (and there should be a replacement), but the addition of a +1 Crit modifier might do the trick. I think that it would be better, though, to have a selection of new maneuvers the warrior can perform with the weapon, having attained the highest level of skill possible. Something like the examples given in the Complete Warrior (if you have it). It takes more design work, but it is ultimately more rewarding and flavorful for the character and the player, and justifies the significant prerequisites for the ability.
All that said, the rest seems really good. I think that in a semi-AU context, it could work really well, and is more interesting and powerful than the fighter (a good thing, I think).
By the way, if you ever have the time, I would really like to see the journeyman class. I like the idea of the Akashic, but I don't like the mystical new-agey flavor. Post it if you are willing.
