Half caster level (Ranger, Paladin, etc) is no longer a thing. Such classes have a caster level equal to their class level. Their class level minus 3 is also acceptable, but such classes need nice things.
Does not gain a Constitution bonus when raging. Instead, gains +2 Fortitude, +2 to Constitution checks, and temporary hit points equal to 2 per hit die, which go away when the rage ends. These bonuses go up to 3 with Greater Rage and 4 with Mighty Rage. This eliminates "oops, my rage ended, now I'm dead" syndrome, and as a side-effect allows undead barbarians to be more effective.
Alternately, because Barbarian is a common dip for Con-focused builds that benefit in other ways from Con boosts, Barbarian keeps the Constitution bonus, all temporary Constitution bonuses that have durations (so Barbarian's Rage and Bear's Endurance but not Amulets of Health) grant temporary hit points (which expire when the Con bonus does) instead of real hit points.
Qualifies for metabreath feats without requiring Power Surge or other shenanigans to acquire a breath weapon with a timer.
Add Knowledge(arcana) to class skills. It just makes sense for a class that worships dragons to have knowledge about dragons.
Add Knowledge(geography) to class skills. Makes sense for a druid to understand the lay of the land.
This, the most powerful class, also asks for a nerf. There are two decent (but probably mutually exclusive) nerfs you can try:
The less extreme nerf is to give Druid animal companion progression as a Ranger.
The more extreme nerf is to say "Spellcasting; Animal Companion; Wild Shape: Pick any two."
Add Knowledge(religion) to class skills. On the one hand, you wouldn't necessarily expect a Favored Soul, granted power by a deity without asking for it, to actually know anything about deities. On the other hand, such Favored Souls can simply not put ranks in Knowledge(religion).
Gains a fighter bonus feat every level, instead of 1st and every even level. This doesn't bump Fighter up a tier or anything, but at least now you don't have any dead levels on your way to Dungeoncrasher, and it's a "however many feats you want"-level dip instead of a 2-level dip.
Knows their entire spell list and casts spontaneously, like a Warmage or Beguiler. (I rejigger Healer a little more completely than this, but this is a solid start.)
Hexblade's Curse usable per encounter rather than per day.
Add Knowledge(history) to class skills.
I personally nerf Leadership for everybody else, and then un-nerf it for Marshal. You could also consider giving Leadership to Marshal as a bonus feat.
Full BAB. Literally the least you can do for this sad, sad class.
Smite Evil per encounter rather than per day. Consider giving this to everything with a Smite ability, such as Soulborn (see below) and Fiendish/Celestial creatures.
Remove Disease per day rather than per week.
When a character uses Smite Evil, the attack also counts as Good for the purpose of bypassing DR/Good. The same applies to all aligned Smites, e.g. Smite Good bypasses DR/Evil.
EDIT 7/26/2017: Player picks either Charisma or Wisdom. Spellcasting and all defaultly Charisma-based abilities all key off whichever they pick. Make the paladin slightly less MAD.
Animal Companion progression at first level, progressing as druid, not as one-half druid.
Gestalt the Samurai from Oriental Adventures with the one from Complete Warrior.
Gain Eschew Materials as a bonus feat at level 1.
Wizards and Sorcerers may begin play with a familiar without having to pay the 100gp cost. Acquiring a familiar after play begins, replacing a familiar, or acquiring a familiar through the Obtain Familiar feat still costs 100gp. Many people don't realize this is a house rule, that Wizards and Sorcerers are supposed to either pony up 100gp when play begins or start without a familiar.
Any prestige class level that advances Wizard or Sorcerer spellcasting also advances familiar abilities as if it were a level of Wizard or Sorcerer. (This is as if all Wizards and Sorcerers took the Forlorn flaw and the Obtain Familiar feat.)
Smite Opposition per encounter rather than per day.
Proficient with bucklers. IT'S RIGHT THERE IN THE NAME, DAGNABIT.
Skill points: the usual x4 at 1st level, not x6. Obvious typo is obviously a typo.
A Wizard specializing in Divination must choose two banned schools, as with every other school specialization, instead of one. Splatbooks give enough Divination options, and "Scry and Die" so favored a tactic, that it's no longer a trash school like it was thought to be in the early days of 3.5.
Also, see familiar stuff under Sorcerer.