Some decent changes overall, I'll just comment of the classes for now, the rules changes in general seem sound and nothing too drastic there. I do have to say that I'm glad you're chainging alot of abilities to 'per encounter' The old system of per day (whether it be one time or a couple of rounds) is archaic and ultimately takes away from the fun. Honestly sometimes people get too bogged down in the hard line rules and dont stop to take a step back to make sure that your supposedly heroic characters are having a blast.
Classes
Bard - At 4th level the bard gains inspire resiliance. This is a bardic music ability that gives all allies that can hear the bard temporary hit points equal to the bard's character level or twice the bard's character level if they are below half of their current maximum hit point total. At 16th level, the bard gains motivating song. The bardic music ability gives all allies that can hear the bard, an immediate attack that does not count against their actions for the round. In addition, bardic music requires a swift action to activate, and lasts for the entire encounter.
Nice changes, the swift action activation of bardic music shoudl be ore and I know many people have already houseruled this as such. In my own setting I made changes similar to this and gave bards the Bardic Knack variant without taking anythign from them.
Barbarian - Barbarian rage lasts for the entire encounter.
works well.
Cleric - Cleric's gain the healing burst ability at 1st level. This ability requires a swift action to activate. Healing burst allows a cleric to lose any prepared spell except domain spells to cure 3 hp per spell level to all allies within thirty feat of the cleric. Turn undead causes 1d6 points of holy damage per cleric level to undead within 30 ft of the cleric. They get a will save for half damage. The DC is 10 + half cleric level + cha bonus. Improved turning adds +2 to this DC. Undead with turn resistance add that number to their save vs. turning. Rebuke and command undead are unchanged. Greater turning (from the Sun domain or another source) deals 2d6 points of holy damage per cleric level.
I like the change to turning, I never ever liked the idea of just making undead run away..its so anti-climatic.
Druid - Druids lose the animal companion and wild shape abilities. Instead they acquire the shapeshifter alternate class feature found in PHBII at 5th level. They also lose the ability to spontaneously cast summon nature's ally spells. Instead they can lose a prepared spell as a swift action to grant all allies fast healing 1 per spell level sacrificed for the duration of the encounter. This ability is called aura of vitality.
Again the shapechange rules should be core, good choice for a change.
Fighter - Fighters gain an abiltiy called combat expert at 3rd level. This ability gives them a +1 competence bonus on all opposed attack rolls or physical ability checks. This abiltiiy improves to +2 at 7th level and and additional +1 every 4 levels. At 5th level a fighter gains elaborate parry. When an attack would normally hit the fighter, he can roll an attack roll. The result of the attack roll is the AC the opponent must beat to hit the fighter. This ability is an immediate action that is usable once per encounter. At 9th level a fighter gains the counterstrike ability. Once per encounter, he may choose to use this ability to deal the maximum amount of damage to an opponent that dealt damage to him in the previous round. The fighter must declare that he is using this ability before he attacks. If he misses the ability is still used up for the remainder of the encounter. Fighters gain an ability called resolve at 11th level that grants them a +4 competence bonus to will saves. At 13th level, the fighter gains the lightning recovery ability. Any time a fighter misses with an attack, he can immediately make another attack with a +2 bonus to the attack roll. This is an immediate action that is useable once per day. At 15 level the fighter gains the augmented critical ability. This abiltiy increases the critical multiplier of any weapon they wield by one step. At 20th level, fighters gain overwhelming assault. As a full-round action, the fighter gains an immediate extra attack every time he strikes an opponent with a -2 penalty, until he misses. A fighter must declare he is using this ability before making his first attack roll. All attacks must made against the same opponent. This ability is usable once per day.
There are so many fighter fixes that hey, whatever works for your campaign is cool. I would suggest giving fighters an ability akin to the Warblade one in which they can switch their 'main' weapons each morning and tranfer their feats to the new weapon they trained with.
Monk - Monks gain an ability called Kiai Strike at 5th level. This ability is useable once per encouter. A monk must delcare he is using this ability before his attack roll. He adds his wisdom modifier to attack and deals his monk level in extra damage. Monk's also gain the decisive strike ability from PHBII at first level. In any given round they can choose to use flurry of blows or decisive strike.
Still pretty bland here, perhaps give them full BaB so they can actuallt hit with these attacks...honestly if you want to make the monk a viable choice then take a look at the swordsage, with the right martial manuevers he becomes what the monk should be.
Paladin - Paladins lose their turn undead, call mount, and spellcasting ability. Smite evil is changed to smite and works regardless of the alignment of the target. Smite is usuable once per encounter at 1st level, twice per encounter at 10th level, and three times per encounter at 20th level. Paladins gain the knight's challenge and shield block abilties of a knight (PHBII) of their level.
This works, I think the loss of the mount is a but much but if it works for the feel you want in the paladins of your setting then more power to ya.
Ranger - Rangers lose their animal companion, combat style, and spelllcasting. Instead they acquire the skirmish ability as a scout of their level.
Honestly I would just take the spellcasting ability out, skirmish can become another combat style for them to choose. But with just spellcasting gone it balances pretty well. I also added a new combat style to my own rangers, Mobility at 2nd....Spring Attack at 6th.....Bounding Assault at 11th......Rapid Blitz at 17th. And gave them the choice of another two wepaon feat or archery feat at 17th (depending on their style)
Rogue - Rogues gain poison use at 4th level. They also gain hide in plain sight at 14th level.
This is okay, just eh. I give em improved feint at 5th and a bonus feat from a rogue feat list at 7th 13th and 18th...also added more specail abilities for them to choose from...Flank everywhere (if you and an ally threaten a creature its considered flanked) is just one example.
Sorcerer - Sorcerers lose the summon familiar ability and gain the ability to apply metamagic feats to spells without taking a full-round action. Sorcerers gain a heritage feat as a bonus feat at 1st level.
good start on changes, I give em reserve or heritage feats every 5th level as well as eschew materials for free...and yeah no more full round metamagic.
Wizard - The reserve feats from Complete Mage are added to list of bonus feats that wizards can take every five levels.
wizards work, as does this one.
Overall the changes look cool, I'll comment on your rules changes later on, but they seem to be alright with maybe the exception of TWF...but thats one of those rules you either love or hate.
