I've been playing around with some ideas in my head for some time now... and I wanted to get some feedback on them...
This will mostly affect spellcasters, though some of my ideas are for mundanes as well...
Cantrips: All 0-level spells become at-will Cantrips. Casting classes that normally do not gain 0-level spells may pick 5 cantrips from any class list of the same casting type. Therefore a paladin may only choose cantrips available to Divine casters and a Spellthief may only choose cantrips available to an Arcane caster.
Caster Levels: Caster levels of the same casting types stack, Caster levels of differing types stack at 1/2 CL (Rounded down). Every 3 levels of a non-caster class adds 1 to any CLs you have, this is always added AFTER any stacking mechanics. Therefore a Wizard 4/Sorcerer 2 would have an Arcane CL of 6 whereas a Wizard 4/Cleric 2 would have an Arcane CL of 5 and a Divine CL of 4, likewise a Wizard 3/Fighter 3 would have an Arcane CL of 4. A Wizard 3/Fighter 3/Cleric 1 would have an Arcane CL of 4 {3 + (1/2x1) + (1/3x3) = 4} and a Divine CL of 3 {1 + (1/2x3) + (1/3x3) = 3}.
Spell Save DC: All spell saves will have a DC of 10+1/2HD+Key Attribute+Spell Level, this is to help keep spell save DCs competitive with save bonuses.
Spell Slots & Spell Points: All spontaneous spell casters use Spell Points to cast spells instead of spell slots. Prepared spell casters use both spell points and spell slots. A Prepared spell caster gains their spell slots from class levels and their spell points from their ability score. Prepared spell casters may cast spontaneously with their spell points but must prepare their spell slots to make use of them.
Note - Under this system Clerics, Druids, & Paladins are considered spontaneous spell casters.
Meta Magic: Spontaneous spell casters may use meta magic without increasing the casting time of the spell. Prepared spell casters MUST prepare their meta magic spells in spell slots, but may spontaneously cast any prepared meta magic spell with spell points. A prepared spell caster may not spontaneously apply meta magic unless granted the ability by a feat or prestige class.
Familiars: Classes that grant Familiars now get the Obtain Familiar and Improved Familiar feats instead. Classes with special familiars modify the Obtain Familiar feat to grant their special familiar instead, but otherwise reference the feat for progression.
Specialist Wizards: Specialist Wizards may add 1/2 their max spell level (rounded up [+1 for 1st lv, +5 for 9th lv]) to the DC of any spell of their specialist school regardless of spell level. You may also benefit from the wizard variants outlined in Unearthed Arcana without giving up wizard class features.
Generalist Wizards: Gain the Elvin Generalist substitution levels regardless of race. Additionally feat progression of a Generalist Wizard is changed to match that of a Martial Wizard.
Domains Spells & Specialist Spell Slots: No change, these bonus slots still function exactly as the book outlines them.
Domain Wizards: Domain Wizards sacrifice the Generalist Wizard benefits for their Domain.
Mundane Class Features: Any basic class feature that improves with levels, and is obtained within the first 3 levels of the class, such as a Rogues Sneak Attack or a Barbarians Rage Continues to improve as if you had gained 1/3 of all other class levels (that do not grant progression of the same ability). So a Rogue 6/Barbarian 3 would have a Sneak Attack of 4d6, could Rage 2/day, and Trapsense +3. However a Rogue 6/Spellthief 3 would still only have a Sneak Attack of 4d6, you would not add 1/2 Spellthief to Rogue for Sneak Attack nor would you add 1/2 Rogue to Spelltheif for Sneak Attack, you would however add 1/2 Rogue to Spelltheif to progress the Spellthief's steal spell & Spellgrace abilties and 1/2 Spellthief to Rogue for the Rogue's Trapsense ability. A 10th Level Rogue cannot improve their Special Abilities class feature in this manner as the ability was not acquired within the first 3 levels of the Rogue class.
Note - Casting abilities are NOT increased in this manner and may only be improved by taking levels of an appropriate casting class.
Saves: -1 to all Good Saves from multi-classing. Your starting class will always progress as normal, but any additional classes will grant good saves at 1 less. Wizard 4/Rogue 2 will have saves of Fort +1/Ref +3/Will +4. What this boils down to is at any character level besides 1st you may not gain more than +1 to any save from class levels.
Multi-class Casting (Abilities): Unless stated otherwise, use the appropriate casting class when calculating variables for any and all spells. A Wizard 4/Sorcerer 2 would not add their Charisma to the spell save of any spell cast as a wizard.
Multi-class Casting (Spells Known): Your spell lists are NOT shared across classes, however, you may use spell slots to prepare any spells known so long as they are of the same casting type. A Wizard cannot prepare Divine spells and an Archivist cannot prepare Arcane spells.
Multi-class Casting (Progression): Add 1/4 of all other casting classes to each casting class to determine the level of spells available in that class. A Wizard 4/Sorcerer 4 would have access to 3rd level Wizard spells and 2nd level Sorcerer spells, a Wizard 4/Cleric 4 would have access to 3rd level Wizard & Cleric spells.
Note - Spells must still be learned as normal.
Other Casters (Psionics, Incarnum, Binding, etc...): Apply the same changes outlined in the Caster Level, Spell Save DC, & Multi-class Casting sections as appropriate.