I was doing my own rewrite of 3E a while ago, but got busy after my son was born. There were some major departures from 3E though, including:
Only 4 classes total. Warrior, Devoted, Rogue, Adept. Warriors had combat abilities, devoted got powers with a pool of points to use them, rogues got tricks and skill masteries, adepts got spells.
There were class feats to turn classes into the more specialized classes like Warrior into Barbarian, or Devoted into Cleric, and other class feats just improved the abilities the base class had. Subclass feats could give powers to non-devoted class, or spells to non-adept classes. Class feats were gained at certain levels, while Adventuring feats were gained at other levels.
Adventuring feats were more generic than class feats that anyone could choose with a few exceptions, or racial feats that enhanced abilities you start with, like elf stealth, or added new abilities at higher levels, like dwarf stone-shaping. I initially wanted a replacement for the word feat, but never came up with something better.
No skill points, and no skill list. Each class had a single skill named for the class that automatically improved with level. The class skill is given a short list of general activities it applies to, with subclasses adding more activities to the list. Rogues may be able to create disguises, while the Thief subclass may add forging documents to the list, for example. In addition to your class skill, non-humans also had a racial skill with its own set of activities it applied to. The dwarf skill would cover their noticing unusual stonework, for example. There were also background skills, with humans getting more of them because of the lack of racial skill. They were described by the player (no set list), but were more specialized than the other types of skills, so a character may have been a blacksmith or chef before adventuring, so would get skills for those activities.
Magic equipment were never vanilla +x items. Each had a number of properties and/or powers. Properties applied all the time, while powers had to be activated. The higher the + bonus, the more properties and powers the item would have. 3E mostly already had this, but I restructured it to my liking.
Never got around to changing spells or monsters.