I have only had time to read these two sections in depth. Following are my first impression thoughts. Obviously, some of this is subject to change based on the rest of the document, which I hope to have time to read soon. Also, note that I did not color my thoughts based on Paizo's desire to remain backwards compatible with the 3.5 OGL material. Frankly, I could care less if you do.
Races
Abilities: Modifiers generally seem okay, although I disagree with a Wisdom bonus for half-orcs. Would it be possible for half-orcs to have +2 Strength, +2 Constitution, and -2 Intelligence - yes it is warrior-centric, but so are half-orcs.
Speed: I suggest giving half-orcs 35 feet base speed and halflings 25 feet base speed.
Skills: Circumstantial skill bonuses are always extra work to keep track of. Half the time, players forget them anyway. I'm not sure what design intent is with taste and smell Perception bonuses. I suggest dropping all circumstantial Perception bonuses and giving elves and half-elves a flat +1 to Perception and giving dwarves a +2 when underground. Also, do dwarves need Craft and Profession with stone added to their class skill lists? For which classes are Craft and Profession not class skills? Are there other circumstantial bonuses that can be made flat bonuses?
Weapons: Half-orcs get proficiency in some nice martial weapons. Dwarves and elves also get martial weapon proficiencies, but generally not in two-handed melee weapons. Humans should get a weapon proficiency.
Languages: I suggest allowing humans to pick a second language; maybe limit choices to racial languages. Why can halflings choose Abyssal as a bonus language?
Favored Class: I suggest allowing humans to pick two favored classes, one of which must be their starting class, and gain the benefit when they take a level in either. Half-elves' favored class should be their starting class.
(Dwarf) Greed: This could be too powerful (essentially a "free" trained skill). Maybe change to flat bonus.
Orc Ferocity: I suggest changing Orc Ferocity to allow an immediate melee attack the first time each day that the half-orc is reduced below 0 hp. This is nearly the same effect, with less to keep track of. Note I have yet to see how dying and death are handled.
Classes
Cleric
Skills: Clerics have 2+Int trained skills, and 10 skills on their class list (not counting Craft and Profession). Of these, at least three (Heal, Religion, and Spellcraft) appear to be "required". Others, such as Appraise, Diplomacy, and either History or Nobility would be great for RP. That does not leave much flexibility. I suggest increasing their base skills to four. I don't think they need Knowledge (arcana) as a class skill.
Orisons: I am fine with the idea of casting orisons an unlimited number of times. However, most orisons have little impact in a high-level game (resistance might be the exception), so I'm unsure about the practical value of this feature. I think WotC's reserve feats were a better 3e approach to at will powers.
Domain Powers: (coming later)
Turn/Rebuke Undead: (coming later)
Fighter
Skills: Fighters have 2+Int trained skills, and 8 skills on their class list (not counting Craft and Profession). None of the fighter's skills seem to be "required", so the base skill number is acceptable.
Armor Training: Selecting a type of armor is not really necessary. How many fighters are switching armor type on a regular basis? Most characters will put all of the bonus into one type of armor. Why not just grant a general defensive bonus and reduce the armor penalty. The total bonus is +4 at 15th level, which outwardly seems reasonable.
Weapon Training: Grants +1 to attack and damage with weapons in a given group. There is more likelihood that a character will pick up multiple groups here than with armor - maybe +3 to primary and +1 to secondary. However, granting fighters attack bonuses is not really necessary. They can already hit much more often than other classes. The attack bonus will just be subsumed in Power Attacks, effectively making this a +2 or +3 (with 2-handed weapon) damage bonus at each interval. As monster ACs increase to compensate for deadlier fighters, the other classes will be left further behind the fighter in melee combat. I would rather see the fighter get abilities or maneuvers that are more specialized than just a generic attack/damage increase. Yes, that is somewhat redundant with the role of feats - something more needs to be done to make the fighter's abilities different from fighter-exclusive feats that every fighter ends up getting. There should be more to make them special.
Armor Mastery: I have no problem with DR 10/-. Again, drop the armor type requirement, it is unnecessary. I would rather see this build up, though, maybe from DR 2/- at 3rd level to DR 10/- at 19th level. Just suddenly adding this ability doesn't work for me.
Weapon Mastery: I don't find this ability compelling enough to wait to 20th level for. There are already spells (bless weapon) and feats (Improved Critical) that accomplish much the same thing. Again, there is the problem of the fighter's abilities seeming very similar to feats. I think more thought is required to differentiate what the fighter can do from what others can do.
Rogue
Skills: Rogue have 8+Int trained skills, and 19 skills on their class list (not counting Craft and Profession); however, Disable Device, Perception, and Stealth are probably the only "required" skills. This gives the rogue a good amount of flexibility.
Sneak attack: I like having sneak attack apply to a wider range of creatures.
Rogue Talents:
The only purpose of finesse rogue appears to be to allow the rogue to take Weapon Finesse at second level without multi-classing to fighter. Why not just allow first level rogues to take that feat as one of their normal feats? Same with weapon training. Besides, most rogues will benefit more from Weapon Finesse than Weapon Focus. Let them take Weapon Finesse at first and Weapon Focus as their 3rd level feat if they really want to. There are better options for rogue talents than these two.
I suggest combining fast stealth and ledge walker; neither is very compelling alone as they only negate a +5 increase in the DC. Just going up a few levels or getting a skill-boosting magic item will also negate that +5, so this is only a good choice at very low levels. (In general, I'm opposed to class features that essentially duplicate a low cost, commonly available item; class features should be reserved for things you can't do any other way.) Alternatives might be something that gives the rogue a climb speed (and corresponding +8 bonus on Climb checks).
I don't like minor magic. I can think of few compelling spell choices. Major magic has more possibilities with spells like magic weapon and true strike. This would of course be better if the spell could be cast as a swift action. Other spells that would be worth learning include the swift spells, like swift expeditious retreat and swift fly and some abjurations like mage armor or shield. I suggest creating a list of available spells for this power. Also, let's make it a supernatural ability rather than spell-like so it won't provoke attacks of opportunity.
I like bleeding attack and slow reactions. There should be more abilities like this that tweak the opponent in the round after a sneak attack. This keeps the rogue more mobile on the battlefield. Dazing, slowing, and shifting (you or them) are all good options. Ability damage is a pain to track, so let's not go there (I'm looking at you, crippling strike).
I don't like resiliency; temporary hit points are a nuisance. Keep defensive roll instead, but make it automatically succeed and allow the rogue to shift while using it. E.g., Defensive Roll (Ex): Once per day as an immediate action the first time an attack would reduce the rogue below 0 hp, the rogue shifts one square and takes no damage from that attack.
There is already a feat (I forgot the name) in one of the spatbooks that is better than stand up. It allows the prone character to regain his footing and attack without provoking an AoO. Perhaps stand up can be combined with rogue crawl to enable a prone rogue to shift and stand while prone as a move action (or even as a swift action). I wouldn't be worried about game balance with this one - how often is the average rogue knocked prone, anyways?
Likewise, surprise attacks doesn't do much for me. Yes, I see the reasoning - more sneak attack opportunities. However, I'm betting a good rogue goes into most surprise rounds either invisible or with cover (and hence practically invisible). Also, a surprise round implies someone is surprised. But if the enemies are acting in the surprise round, it obviously wasn't them. This ability seems to perversely reward the rogue for having easily surprised companions! Instead, how about once per day the rogue can add half her class level as a bonus to one initiative roll. If that's not good enough, let her decide to do it after initiative has been rolled and revealed - that way the rogue has a good chance of going first in the combat where she uses this ability. This would be a very compelling ability at high levels.
Opportunist can be useful, but it could also be better. How about allow the rogue an AoO whenever someone misses her (subject to normal per round limitations). Definitely save up for that cloak of displacement now!
There is a splatbook feat that allows a character with evasion to move and hide after evading an area effect. That would be a good one to include as a rogue talent - if only to keep it more rogue only.
Rogues also need a better way to get sneak attack off after the first round without a flanking partner (because some players just don't know how to set a flank). Improved Feint is not good enough - it leaves the rogue vulnerable since it eats up his move action. Rogue's need to be able to feint, move, and attack in the same round. This is powerful enough, however, that a speed limitation may be necessary (e.g., once per encounter), or maybe only allow it with a charge action (so the rogue gives up some defense and flexibility to do it).
Does the statement that a rogue cannot select a rogue talent more than once prohibit a rogue from gaining multiple combat maneuver feats? Is that the intent?
Master Strike: Okay, I'm sorry but I don't like save or die effects. Even worse, I think, are save or die effects that only succeed once in a blue moon. The average DC for this guy will be about 25. Most CR 20 monsters can make that rather easily. I'm not sure you go all the way to 20th level for that. Some better options: auto stun for one round (allows the rogue to land another sneak attack and another and another until someone comes to help the poor monster), creature gives up an AoO to all characters threatening it (rogue opens it up, fighter brings it down - I like teamwork, it makes players pay attention when it isn't their turn).
Wizard
Skills: Wizards have 2+Int trained skills, and 13 skills on their class list (not counting Craft and Profession). Since wizards typically have high Intelligence, they will probably never be at a loss for essential skills.
Cantrips: I have no problem with using prepared cantrips at will, but see above discussion for cleric orisons.
Note: I have not yet had time to look at the cleric domain powers or wizard school powers.
