I just finished reading over the document. I like the idea of feat based magic. However I feel this execution does need a bit of work yet.
I have heard that an acid test of a feat's power level (or balance) is this. If no one will ever take the feat it is too weak and conversely if everyone wants to take the feat it is too powerful. With this in mind I feel that the basic spell casting feat is too powerful. I cannot imagine any character, who meets the prereqs, not taking this feat.
I believe a basic analysis, number crunch, will demonstrate my concerns with this.
At each level a character gains 1dX + Wis will points.
Since you state that will points are gained in much the same way as hit points I assume that means that you get max will points at first level.
Here is the Spell Use, Basic Feat
SPELL USE, BASIC [general]
You have the ability to cast low-level spells.
Prerequisites: Intelligence 11+.
Benefit: Choose two schools of magic, plus a number of additional schools equal to your Dexterity bonus. If your Dexterity bonus is ?2 or lower, you may still choose one school of magic. You have the ability to cast 0th-level, 1st-level, and 2nd-level spells from the chosen schools. You can learn three 0th-level spells, plus a number of additional spells equal to your Intelligence modifier. You can learn two 1st-level spells, plus a number of additional spells equal to your Intelligence modifier. You can learn one 2nd-level spell, plus a number of additional spells equal to your Intelligence modifier. Casting a 0th-level spell burns 1 Will Point. Casting a 1st-level spell burns 2d4 Will Points. Casting a 2nd-level spell burns 2d6 Will Points, or 6d6 Will Points if you are not yet character level 3+.
Let?s look at a third level rogue with 12 for all relevant statistics who has the average will points.
Will Points (6+1 + 3+1 + 3+1) = 15 will points
If this rogue took spell use, basic then they would learn 4 zero level spells, 3 first level spells and two second level spells. The would be allowed to take three schools of magic.
This is plenty for them to learn all of the ?Rogue? spells like arcane lock, move silently, etc.
By 20th level this rogue, still sticking with averages, would have (6+1 + 57+19) 83 will points. Danananananana super rogue.
I could easily carry this example out to all the classes, but I think this makes the point especially since this example doesn?t even push the limits of the system and already breaks it.
I recommend doing something to increase the cost of basic spell casting. Either force the person to take some ranks in spellcraft. Maybe instead of using character level for when a character can safely cast spells of a given level make it contingent upon ranks in spellcraft. 4 ranks = lvl 1, 6 ranks = lvl 2, 8 ranks = lvl 3, etc. I think that would significantly increase the cost of casting skills. Another way to do it is that not every character gets will points. Instead they have to burn a feat to get them and some classes get the feat for free at first level, but this may cause an over population of battle-mages.
I think that the Sage class is significantly over powered.
At every other level they get a bonus feat and at the levels where they don?t get a bonus feat they get a discovery. They get a d6 hit die, d8 will die, and 6+int skill points. This is too much IMHO. I recommend giving them a d4, 4+int skill points and remove the ability to add a class skill, with retroactive point change, from the discovery list. The drawbacks to arcane secret a purely role-playing based. It is not a good idea to give a mechanical benefit with only a role-playing detriment. If this took con points permanently form the character and gave them the physical deformity off the chart to represent the con loss that could be good. Maybe -2 con points for each time this discovery is made.
Other then these two things it is an excellent system though.
I do have some formatting pointers though.
1) PAGE NUMBERS 19 pages without number, what if your print out gets out of order?
2) Shade every other row on the tables, it makes it a lot easier on the reader.
3) Wrap text around the tables that don?t take up an entire page to make the document shorter.
You really don?t need to include the spell lists for each school. You haven?t changed the schools of any of the spells so this is unnecessary and just wastes printer ink.