There are so many... How can I list them all?
ALL classes receive one "Professional" Feat from a special, class-only list at first, fifth, tenth, fifteenth, and twentieth levels (just like the wizard does, now, but a different list for each class).
ALL classes have one or more Knowledge skills as class skills. Fighters get Knowledge (History) - as it states that it includes knowledge of battles - Clerics and Paladins Knowledge (Religion), Barbarians, Druids, and Rangers Knowledge (Nature), Bards, Sorcerers and Wizards all knowledge skills, etc.
ALL classes with two skill points get theirs doubled, and all the rest get an increase.
Clerics get more Domains as they rise in level, and special abilities related to them.
Druids have the ability to Speak with Animals at will. A better explanation of their weapon and armor restrictions is included in the class write-up.
Fighters, Barbarians, Paladins and Rangers receive Bluff and Intimidate as class skills.
Rangers get a total re-write (don't even get me started!) Balance and Knowledge (Geography), at least, are added as class skills. Their role in the party is clearly stated in the class write-up.
Monks get to choose their special abilities from a selected list.
Fighters get some other abilities besides just fighting.
Permanent Energy Level/Ability Drain is removed.
Magic items granting skill boosts are now limited to Level+3 Ranks, up to the stated maximum. Thus, a Ring of Jumping at first level grants +4, not +30. This makes the Rogue who has maxed Jump skill no longer invalidated.
Return to the system that +1/+2 weapons are made of steel/whatever, +3 are Meteoric Iron, +4 Mithril-alloyed Steel, +5 pure Mithril or Adamantite-alloyed steel, and pure adamantite are +6 (Epic level). Thus, those unmagical mithril chain shirts will be MUCH more expensive (Bilbo/Frodo's in The Hobbit/The Lord of the Rings was stated to be worth more than the entire Shire, and Gimli said that that was under-valuing it)!
Remove the rule that, in order to make a Spellcraft check, one must wait until after the spell has been cast! This makes no sense especially when counter-spelling!
Make the weapon and equipment weights more realistic. They do *NOT* weigh 25#! Even a solid metal handaxe doesn't weigh five pounds! That's more than a sword!
I'm sure there are many more...