As it stands, there isn't a lot of difference between wizards and sorcerers. Sure, I know, they're Core, and they've differentiated caster classes since then, but still...
Look at the fluff. Wizards learn to wield magic, sorcerers develop magical powers naturally, usually due to odd ancestry.
In my view this means that wizards, having a greater understanding of magic, can learn to manipulate it far better than a sorcerer can. However, in the end magic will always be something alien to them, and they will never be able to match a sorcerer in raw power. If both can shoot fire from their hands, both a wizard and a sorcerer could conceivably learn to shape the fire into a sword. The wizard would probably create a detailed replica of a mundane longsword from some learned pattern, while the sorcerer ends up with a giant greatsword-shaped mass of flames. However, only a wizard could manipulate magic at such a fundamental level that he could shoot
ice from his hands instead. The sorcerer can shoot fire because the blood of red dragons flows through his veins - channeling the burning power of red dragons to shoot ice would be weird.
[spoiler]A good example is
Kekkaishi - it has two main characters who have the same basic power (creating cube-shaped forcefields which can be imploded on enemies) but use it very differently. Yoshimori has plenty of stamina and power, but poor accuracy and speed. He also tends to use too much power without meaning to. By contrast, if Tokine is trying to trap a monster the size of a mosquito she will make a kekkai around it
exactly the size of a mosquito, with no energy wasted. She eventually gets jealous of how durable his kekkai are and learns a technique which lets her create three layers around a target at once, but using it even once leaves her exhausted. Yoshimori takes longer to learn the technique, but uses it much more effectively. (Tokine makes up for it by learning how to shape her kekkai into long "spears", something which does not require much power and which Yoshimori does not have enough control to do)[/spoiler]
Now, some of this is covered already. Wizards have a potentially limitless spell selection, and get bonus feats they can use for metamagic or to encode magic into items. Sorcerers get more spells per day and fewer restrictions on when they can use them. However, I don't feel like this is enough. The underlying archetypes can be used as a guide for further mechanics. Plus, there are some problems with the ways they've been differentiated already. For instance, wizards find it easier to Heighten or Empower spells than sorcerers (they get bonus feats, and don't increase their casting time).
I would incorporate the effects of Heighten Spell and Eschew Materials into the sorcerer's spellcasting mechanism (ie. they aren't modifying the formula of a spell when they heighten it, their formula just doesn't specify an upper limit on the energy they put into it). Empower Spell I'm a little less sure of - maybe sorcerers' spells should just be more powerful to begin with, with a Warmage Edge style ability based on Charisma (I recommend making the bonus Cha mod x spell level). A d6 Hit Die would also help.
If you have ever made a rewrite of the wizard or sorcerer classes, what ideas have you used?