This was how I was planning to fix the "polymorph problem" in my own game:
Polymorph School: Polymorph spells change one thing into another. While natural shapechangers can be affected, those with the Shapechanger creature subtype can always choose to revert back to their own form once it is their action.
Many polymorph spells have a limitation to change into another creature equal to HD + LA (Level Adjustment). If a creature does not have a listed LA, you can use the table below to estimate the LA of a given creature. The GM has final say in the LA of any creature.
Ability LA
Natural flight +1
Natural armor +1
Greater than 5 ft. reach +1
Unbalanced ability scores(1) +1
Special Attack (per 2 abilities) +1
Special Qualities (per 3 abilities) +1
Racial skill bonus +1
Animal type -1
Size small or smaller -1
(1) “Unbalanced” means that the total ability modifiers add up to greater than +0. Add in a +1 LA for every +1 ability modifier (i.e. +2 to attributes) total above the creature’s HD.
(Note: this was just me free-form guessing based on the chapter in Savage Species. I'm sure the design team would have a much better grip on what would constitute an LA adjustment for the table above)
Alter Self
Transmutation (Polymorph)
Level: Brd 2, Sor/Wiz 2
Components: V, S
Casting Time: 1 standard action
Range: Personal
Target: You
Duration: 10 min./level (D)
You assume the form of a creature of the same type as your normal form. The new form must be within one size category of your normal size.
Upon gaining this spell, the spellcaster gain 2 forms they can assume with the spell, plus an additional form for each additional level they obtain (Assume the caster can take 20 on the Knowledge check when determining what forms he may choose). These forms cannot exceed the ECL of the caster (HD + Class Levels + LA). The total ECL cannot exceed 10. At each level, the caster may change one of his prior chosen form to a new form. If the caster wishes to make an impromptu change to a creature not on their list of forms, they must make an appropriate Knowledge check to make the change. The Knowledge check is based on the type of creature whose form is to be assumed (i.e., Knowledge [Arcana] check to assume the form of a draconic creature)
Action Knowledge DC
Assume an impromptu form not on character's polymorph list. 20
character is familiar with form (has studied physiology of a "living" specimen for at least 1 hour or more) –5
character has a similiar creature in his form list (such as becoming a lion if you can change into a tiger) –5
character has no visual reference of new form* +5
Character has never encountered creature in–game +5
creature is rare, reclusive, singular (such as the tarrasque) or extraplanar in nature (+2 for each that applies) +2
* Having seen the creature in a book, painting or other 2D depiction does not count as having a visual reference.
You retain your own ability scores. Your class and level, hit points, alignment, base attack bonus, and base save bonuses all remain the same. You retain all supernatural and spell–like special attacks and qualities of your normal form, except for those requiring a body part that the new form does not have (such as a mouth for a breath weapon or eyes for a gaze attack).
You keep all extraordinary special attacks and qualities derived from class levels, but you lose any from your normal form that are not derived from class levels.
If the new form is capable of speech, you can communicate normally. You retain any spellcasting ability you had in your original form, but the new form must be able to speak intelligibly (that is, speak a language) to use verbal components and must have limbs capable of fine manipulation to use somatic or material components.
You acquire the physical qualities of the new form while retaining your own mind. Physical qualities include natural size, mundane movement capabilities (such as burrowing, climbing, walking, swimming, and flight with wings, to a maximum speed of 120 feet for flying or 60 feet for nonflying movement), natural armor bonus, natural weapons (such as claws, bite, and so on), racial skill bonuses, racial bonus feats, and any gross physical qualities (presence or absence of wings, number of extremities, and so forth). A body with extra limbs does not allow you to make more attacks (or more advantageous two–weapon attacks) than normal.
You do not gain any extraordinary special attacks or special qualities not noted above under physical qualities, such as darkvision, low–light vision, blindsense, blindsight, fast healing, regeneration, scent, and so forth.
You do not gain any supernatural special attacks, special qualities, or spell–like abilities of the new form. Your creature type and subtype (if any) remain the same regardless of your new form. You cannot take the form of any creature with a template, even if that template doesn’t change the creature type or subtype.
You can freely designate the new form’s minor physical qualities (such as hair color, hair texture, and skin color) within the normal ranges for a creature of that kind. The new form’s significant physical qualities (such as height, weight, and gender) are also under your control, but they must fall within the norms for the new form’s kind. You are effectively disguised as an average member of the new form’s race. If you use this spell to create a disguise, you get a +10 bonus on your Deception (Disguise) check.
When the change occurs, your equipment, if any, either remains worn or held by the new form (if it is capable of wearing or holding the item), or melds into the new form and becomes nonfunctional. When you revert to your true form, any objects previously melded into the new form reappear in the same location on your body they previously occupied and are once again functional. Any new items you wore in the assumed form and can’t wear in your normal form fall off and land at your feet; any that you could wear in either form or carry in a body part common to both forms at the time of reversion are still held in the same way. Any part of the body or piece of equipment that is separated from the whole reverts to its true form.
Polymorph(P)
Transmutation (Polymorph)
Level: Sor/Wiz 4
Components: V, S, M
Casting Time: 1 standard action
Range: Touch
Target: Willing living creature touched
Duration: 10 min./level (D)
Saving Throw: None
Spell Resistance: No
This spell functions like alter self, except that you change the willing subject into another form of living creature. The new form may be of the same type as the subject or any of the following types: aberration, animal, dragon, fey, giant, humanoid, magical beast, monstrous humanoid, ooze, plant, or vermin.
Upon gaining this spell, the spellcaster gain 2 forms they can assume with the spell, plus an additional form for each additional level they obtain (Assume the caster can take 20 on the Knowledge check when determining what forms he may choose). These forms cannot exceed the ECL of the caster (HD + Class Levels + LA). The total ECL cannot exceed 15. At each level, the caster may change one of his prior chosen form to a new form.
***Optional Rule***
If the caster wishes to make an impromptu change to a creature not on their list of forms, they must make an appropriate Knowledge check to make the change. The Knowledge check is based on the type of creature whose form is to be assumed (i.e., Knowledge [Arcana] check to assume the form of a draconic creature)
Table: Knowledge check to Polymorph
Action Knowledge DC
Assume an impromptu form not on character's polymorph list. 20
character is familiar with form (has studied physiology of a "living" specimen for at least 1 hour or more) –5
character has a similiar creature in his form list (such as becoming a lion if you can change into a tiger) –5
character has no visual reference of new form* +5
Character has never encountered creature in–game +5
creature is rare, reclusive, singular (such as the tarrasque) or extraplanar in nature (+2 for each that applies) +2
* Having seen the creature in a book, painting or other 2D depiction does not count as having a visual reference.
***End Optional Section***
You can’t cause a subject to assume a form smaller than Fine, nor can you cause a subject to assume an incorporeal or gaseous form. The subject’s creature type and subtype (if any) change to match the new form.
Upon changing, the subject regains lost hit points as if it had rested for a night (though this healing does not restore temporary ability damage and provide other benefits of resting; and changing back does not heal the subject further). If slain, the subject reverts to its original form, though it remains dead.
The subject gains the Strength, Dexterity, and Constitution scores of the new form but retains its own Intelligence, Wisdom, and Charisma scores. It also gains all extraordinary special attacks possessed by the form but does not gain the extraordinary special qualities possessed by the new form or any supernatural or spell–like abilities.
Incorporeal or gaseous creatures are immune to being polymorphed, and a creature with the shapechanger subtype can revert to its natural form as a standard action.
Polymorph can be made permanent by a permanency spell, which locks the target in its new form.
Material Component: A bit of fur, scales or other bodily tissue from the creature to become.