(Sorry about the late post. You'd think I could keep up with a monthly schedule, but my life had to go and be stupid on me.)
Now to get into the magic and psionics rules. This is still an area that I am feeling out, but here are my ideas so far.
The major necessity is that is fit together much better with the system that surrounds it. So magic and psionics will both be skill-based, allowing them to improve with use, and will feature milestones in their advancement.
But what will make them different? In most cases, it's not much of an issue, as a game will often feature only one or the other. But universal games, or those with "kitchen-sink" settings often find magic and psionics butting up against each other. And they often suffer for it, typically because the systems are so similar that there's little point in differentiation, or different for the sheer sake of being different.
One conceit that's been used in modern fantasy fiction is the idea that magic and psionics are largely the same thing. People with reliable intuition, poltergeists, medium abilities, and such are simply untrained wizards. This first came to my attention in Simon Hawk's "Wizard" series, but has also shown up in the more recent and more popular "Dresden Files" novel (notably "White Night").
But those stories present psychic ability as a lesser form of the power, and if you're going to be anything, you become a wizard. Trade in your intuition for divination spells. Telekinesis gets channeled into apportation magic. Which is no fun from a gaming perspective. Players want their psionics to be a valid, equal and interesting choice, not a lesser option.
So let's take that split and refine it. Psychic powers are crude, but powerful. Magic spells are specialized, but efficient. When faced with a locked door, a telekinetic can reach into the lock with his mind and jiggle the parts around until they unlock. A mage in the same position can simply cast a knock spell.
Also, magic is very precise, while psi is flexible. That knock spell is very useful against locked doors, but useless when you're trying to pick up a weapon from across the room. Or trying to move boulders out of the way to save people from a cave-in. It all depends on how many Power Points you're willing to invest in it (Yes, I'm planning on using a Power Point system for magic and psi, in keeping with the source material).
While I've got a good portion of the psionics system figured out (it was actually my initial inspiration for the milestone system), magic is much trickier.
First of all, how are spells learned? Should a milestone grant a number of spells available for casting? Or maybe learning a magic skill gives you access to a specific spell list and you can try to cast any spell on that list, but at a penalty, and milestones allow you to buy off that penalty. And should there be a point at which a skill roll is not needed for the casting of a spell?
I'm sure actual spell lists will come as I develop the game further and get more into the setting.
The next challenge is spell resistance. Rolling against a stat makes a degree of sense, but in a percentile system, chances are pretty low. So someone with a pretty good Dex score (say 25) has only a 25% chance to save against a fireball spell. And once we factor in the contested action mechanic (blackjack percentile rolls), it becomes even more bleak, since a caster can have an 87% chance to cast the spell, and if he rolls anything over 25, that high Dex means nothing.
One potential to this is allowing either resistance skills that can be improved or making milestones available that provide bonuses to magic resistance.