Hello everyone. This is my most major attempt at homebrewing so far, so Great Wall of Text Warning 
I'm thinking that the PrC should require the ability to cast 3rd-level spells (5 class levels for Wizards/Druids/Clerics, 6 for Sorcerors, 7 for Bards, not Paladin/Ranger friendly), and would advance the class's spells/day. It would not provide access to new spells known from the base class's list, since there would be no reason to continue the base class if the PrC gained further access to the base class list in addition to the PrC's new spells. As compensation, the PrC would not only provide additional spells, but also numerous meta-magic feats so that the caster can use their original spells in the higher level slots if they wish to do so instead of only using their new spells.
Also, each Elementalist spell would function as meta-magic spells in the sense that they can be used in any spell slot for differing levels of power (partially to keep the spell lists small enough to be managable while still going from 1st to 9th level slots). However, some extremely powerful spells also take penalties to both Spell and Caster Levels, so if a spell would last for 1 round/[SL+CL] and a 15th level caster (perhaps 5 wizard + 10 elementalist?) prepares it in a 5th level slot, but the spell takes a -2 penalty to effective SL and CL, then the spell only lasts for 13+3=16 rounds instead of 15+5=20. Spells cannot be prepared in a Spell Slot such that the Effective Spell level becomes less than 1, for example: Boulder Missile, which takes no penalites to SL or CL, can be prepared in any Spell Slot except Level 0, however Lava Dragon Apotheosis, taking a -3 penalty to both SL and CL, can only be prepared in at least a 4th level Spell Slot.
I'm thinking that the Elementalist spell list would be divided into 4 basic elements (Earth, Air, Fire, Water), 4 para-elements (Earth/Fire makes Magma, Earth/Water makes Slime, Air/Fire makes Smoke, Air/Water makes Ice), and 4 energies (Fire/Water//Air makes Electricity, Fire/Water//Earth makes Acid, Earth/Air//Water makes Cold, Earth/Air//Fire makes Heat). Each element behaves a specific way, mostly so that there is a tangible, strategic reason to pick each (and so that it's easier to keep track of each spell list if there is a reason for each).
Earth is used for direct defense by physically blocking an enemy. Fire is used for direct offense by physically harming them. Air is used for indirect offense, buffing so that the person does damage better instead of the spell doing it's own damage. Water is used for indirect defense, de-buffing enemies so that they attack less effectively instead of the spell itself stopping them.
However, when an Elementalist learns a para-elemental combination of two elements, s/he can use each element the way that s/he would normally use the other (Example: the Magma spell list contains an Earth spell used for offense and a Fire spell used for defense). Opposing elements cannot be used together except through an intermediary element (Earth and Air cannot be combined directly, but Smoke and Magma can be through Fire), which creates a form of energy. For example, if an Elementalist has access to Smoke (Air/Fire) and Ice (Air/Water), then using Air to keep Fire and Water together creates Electricity spells (Smoke is used as a de-buff the way Water would be; Ice is used as a damage spell the way Fire would be.)
Since this class focuses on replacing the spells that can be learned, I feel that it would benefit Sorcerers more than any other caster. Wizards, Druids, and Clerics can cast any of the dozens of spells that they have the level for and would probably need more slots/day more than they would need even more spells to choose from to fill those slots. Only Bards have fewer spells known than Sorcerors, and their prepared casting + fewer slots/day mean that even these new spells don't go as far as they would for a Sorcerer.
Skills Points at Each Level: 2 + int
Hit Dice: d6
Level | BAB|Fort|Ref|Will | Special | Spells/day
1st | +0|+0|+0|+2 | +1 Element, Metamagic Bonus Feat | +1 Spellcasting class
2nd | +1|+0|+0|+3 | +1 Element | +1 Spellcasting class
3rd | +1|+1|+1|+3 | +1 Paraelement | +1 Spellcasting class
4th | +2|+1|+1|+4 | +1 Element, Metamagic Bonus Feat | +1 Spellcasting class
5th | +2|+1|+1|+4 | +1 Paraelement | +1 Spellcasting class
6th | +3|+2|+2|+5 | +1 Element | +1 Spellcasting class
7th | +3|+2|+2|+5 | +1 Paraelement, +1 Energy, Metamagic Bonus Feat | +1 Spellcasting class
8th | +4|+2|+2|+6 | +1 Paraelement, +1 Energy | +1 Spellcasting class
9th | +4|+3|+3|+6 | +1 Energy | +1 Spellcasting class
10th | +5|+3|+3|+7 | +1 Energy, Metamagic Bonus Feat | +1 Spellcasting class
Spells per day: When a new elementalist level is gained, the character gains new spells per day as if he had also gained a level in any one spellcasting class he belonged to previously. He does not, however, gain any other benefit a character of that class would have gained. This essentially means that he adds the level of elementalist to the level of whatever other spellcasting class the character has, then determines spells per day and caster level accordingly. If a character had more than one spellcasting class before he became an elementalist, he must decide to which class he adds each level of elementalist for the purpose of determining spells per day.
Metamagic Bonus Feat: An Elementalist gains one Metamagic Feat at each of levels 1, 4, 7, and 10.
Spell lists: Elementalist spells are divided into 12 lists (4 for the basic elements * 1 spell each, 4 for the paraelements * 3 spells each, and 4 for the different energies * 3 spells each). At each level, an Elementalist gains access to the appropriate number of spell lists.
At Level 1, an Elementalist gains one of 4 Element spell lists that are available.
For example: You might start with Earth, Air, Fire, or Water
At Level 2, an Elementalist gains one of the 2 Element spell lists that are available.
If you have Earth, then you might add Fire or Water [not Air, which opposes Earth]
At Level 3, an Elementalist gains the Paraelement spell list that is available
If you have Earth and Fire, then you add Earth/Fire (Magma)
At Level 4, an Elementalist gains one of the 2 Element spell lists that are the available
If you have Earth and Fire, then you might add Water or Air
At Level 5, an Elementalist gains the Paraelement spell list that is available
If you have Earth, Fire, Water, and Earth/Fire (Magma), then you add Earth/Water (Slime) [not Smoke or Ice, which require Air]
At Level 6, an Elementalist gains the final Element spell list
If you have Earth, Fire, and Water, then you add Air
At Level 7, an Elementalist gains one of the 2 Paraelement spell lists available, as well as the Energy spell list that becomes available with the chosen Paraelement
If you have Magma and Slime, then you might add Smoke + Magma/Smoke (Heat) or Ice + Slime/Ice (Cold) [not Smoke + Slime/Ice (Cold) or Ice + Magma/Smoke (Heat)]
At Level 8, an Elementalist gains the final Paraelement spell list, as well as one of the 3 available Energy spell lists
If you have Magma, Slime, and Smoke, then you add Ice
If you have Heat, then you might add Electricity, Cold or Acid
At Level 9, an Elementalist gains one of the 2 available Energy spell lists.
If you have Heat and Electricity, then you might add Cold or Acid
At Level 10, an Elementalist gains the final Energy spell list
If you have Heat, Electricity, and Cold, then you add Acid
The spells in each list specifically are as follows:
Elements
- Earth: direct DEF (shield)
- Stone Shield (Conjuration; personal/target, 1 round/CL; V): A large slab of stone hovers next to the target, providing +1/SL armor bonus to AC
- Air: indirect ATK (buff)
- Whirlwind (Trasmutation; personal/touch; 1 round/CL; V): the target of the spell gains a bonus of +1/SL (to AC from dodge if fighting defensively, otherwise to attack rolls) and increases base speed by +5 ft/SL
- Fire: direct ATK (damage)
- Dragon’s Fire (Evocation; 5 ft/SL ray; VS): Line of flame emenating from the caster's arm that deals 1d3/SL + 1/CL damage and risk of catching fire, with the Saving Throw DC to put out the fire increased by +1/SL
- Water: indirect DEF (de-buff)
- Quickwater (Conjuration; close range; target; 1 round/CL; S): Ground water climbs up the target and clings to their body up to their neck, obstructing their movement and inflicting a -1 penalty/SL to any attack/damage rolls