Mana-Based Spellcasting (3.5e Variant Rule)
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Many people have tried to make a good point-based casting system, but they have all failed because of a single design flaw: making higher-level spell costs increase. Increasing spell cost with level requires casters to have absurd amounts of spell points at high levels, which in turn allows them to cast their most powerful spells way too often at the expense of lower-level spells. This works with psionics because the powers are designed with augmentation and a point-based system in mind; redesigning every spell manually requires an unreasonable amount of work and makes the system incompatible with additional material.
The solution, instead of making casting cost increase with spell level, is to make it decrease with caster level.
Mana: You have a pool of this. Casting spells drains from the pool.
Strain Tolerance: This is mana by a different name. Instead of counting mana down, casters accumulate strain points, and have a limit on how many they can accumulate. This is a purely cosmetic change, and can easily be inverted with no mechanical change.
Mana/Strain Cost: This table shows us the mana or strain cost (the costs are identical) of each spell. As you can see, the cost increases slightly with spell level (duh) but decreases with caster level - this is the most important feature of the system, the concept that finally made mana-based casting a real and balanced option.
 The Rules
From here on out, the rules will use strain instead of mana, because it is easier to add than subtract. All unspecified rules (such as spell DCs) are unchanged.
 Strain Tolerance
A spellcaster's strain tolerance equals her primary spellcasting ability score (the ability normally used to determine bonus spells per day), plus 1/2 the sum of her spellcasting levels (including prestige class levels that increase caster level).
 Casting a Spell
Spellcasting taxes both the body and the mind, and this is the basic limiting factor for how many spells can be cast before resting. Every spell has a strain cost, based upon the spellcaster's level and the spell's level, shown in Table: Wizard Strain Costs.
Whenever a spellcaster casts a spell, she accrues strain equal to the spell's strain cost. While her total strain is less than or equal to her strain tolerance, she suffers no ill effect. Casting spells past her strain tolerance, however, is extremely taxing.
When a spellcaster's strain exceeds her strain tolerance, she immediately becomes fatigued (even if she is normally immune to this condition). To cast another spell, a fatigued spellcaster must first make a Fortitude save with a DC equal to 20 + the spell's level + her excess strain. If successful, the spellcaster casts the spell as normal; otherwise, she loses the spell and immediately becomes exhausted (even if she is normally immune to this condition), though she does not accrue strain from the attempt. An exhausted spellcaster cannot cast any spells. An hour of complete rest relieves exhaustion.
If spellcaster normally prepares spells, the "readied spell" is not forgotten and can be cast again as long as the spellcaster has the strain to spare. The advantage of spontaneous spellcasters in this regard is a heightened strain tolerance.
 Recovering Strain
A spellcaster loses strain equal to 1/2 her character level (but never more than her primary spellcasting ability modifier) per hour if she does not cast spells, fight, run, or otherwise exert herself. A spellcaster who is fatigued due to excess strain ceases to be fatigued as soon as her strain no longer exceeds her strain tolerance. However, a spellcaster does not recover strain while exhausted.
A spellcaster recovers much faster when she rests; a full 8 hours of rest removes all strain.
 Example: The Wizard
Strain-based wizards ready spells each day in the same fashion as their spell-slot cousins, but do not lose prepared spells once cast—instead, their spells are limited by their strain tolerance.
(Special note: feats like Versatile Spellcaster (RDr) would not allow you to sacrifice level 3 castings for level 4 castings at level 20, because such feats explicitly deal in spell slots and this variant does away with such a concept.)
 Example: The Sorcerer
The sorcerer's table mirrors the wizard's. However, to compensate for his limited array of spells, he multiplies his Charisma score by 1.5 when calculating his strain tolerance. Thus, the sorcerer can cast more often, but from a smaller selection than the wizard, as usual.