Wizards of the Coast made numerous attempts to errata the unbalanced polymorph spell family in D&D 3.0 and 3.5, before eventually accepting that the spell was inherently broken due to its unbounded versatility. In 2006, Wizards decisively addressed the issue by sidelining polymorph, removing dependencies on the spell throughout the entire game, and introducing less versatile alternatives. This plan was announced by Andy Collins in the February 2006 article, The Polymorph Problem.
In the original D&D 3.0 Player's Handbook (2000), all polymorph spells were based on polymorph other, a Sor/Wiz 4 spell of permanent duration which defined the baseline for what forms polymorph spells allowed and which abilities it could grant. Spells beginning "As polymorph other, except ..." included animal shapes, polymorph any object, polymorph self, and shapechange. The druid's Wild Shape ability was also based on this important spell, as were some monster abilities to change form.
Tome and Blood (2001) introduced updated versions of polymorph other and polymorph self which specifically superceded the versions in the Player's Handbook. Most significantly, this removed a drawback that polymorphed creatures suffer a -2 penalty to most rolls, making it now considerably better and removed a powerful ability of polymorph self to change form at will.
Polymorph other, originally intended to be a "turn the enemy into a toad" offensive spell, was now being used as a permanent, highly versatile buff spell. Why not have the fighter spend the entire adventure in the form of an ogre?
To address this issue, the D&D 3.5 Player's Handbook (2003) divided polymorph other into two spells: the 4th level polymorph, which was now limited to 1 minute per level as typical of a buff spell in D&D 3.5; and the 5th level baleful polymorph, which permanently turned enemies into a small animal such as a toad.
Complicating the polymorph family tree, polymorph was now based on alter self, a 2nd level spell which adopted most of polymorph other's stipulations and effectively became polymorph limited to 5HD and no type changes. Animal shapes, baleful polymorph, polymorph any object and shapechange were now based on polymorph, as was the druid's Wild Shape ability. However, shapechanging monsters now used a polymorph-like ability called Alternate Form, which was decoupled from the polymorph spell.
Interpreting the limits of polymorph-based spells and effects was difficult, and there were many loopholes and ambiguities which players could exploit. Even the more balanced creatures were a problem, since the spell's usefulness increased with the number of monster books available. Wizards of the Coast continued to release monster sourcebooks, and players scoured them for the most useful and broken monsters that fell within the limits of alter self and polymorph.
The Polymorph Problem
Finally, Wizards of the Coast admitted defeat. In a 2006 article titled The Polymorph Problem, Andy Collins declared that polymorph was inherently unfixable:
This problem goes well beyond what can reasonably be fixed by errata. While a fourth take on the polymorph spell might create a spell that didn’t create pages of rules confusion, it won’t correct the “unbounded effect” of the spell’s core function without fundamentally changing the spell’s identity. The ideal “take the form of another creature” spell would limit the caster’s options to a very small list of choices (possibly as low as one). To replace even a reasonable fraction of the total functionality of polymorph, then, would require not one spell but more than a dozen, scattered across various levels and class lists.
An errata was launched for the Player's Handbook. The druid's Wild Shape was now based on the Alternate Form monster ability, and their A Thousand Faces now based on disguise self instead of alter self. Animal shapes and baleful polymorph were decoupled from polymorph, and baleful polymorph was given a risk of memory loss to discourage its use as a buff spell. Shapechange was nerfed from 2x the caster's HD to 1x.
Sourcebooks started to introduce limited polymorph-like spells which allowed on a single, carefully balanced form. Player's Handbook II described the Polymorph subschool, now a generic category defining the base state of shapechanging spells, and included spells like dragonshape and trollshape.
Eberron organized play Mark of Heroes banned polymorph, and the other open-ended shapechanging spells and prestige classes. The reasons cited were that they were too complex to run and adjudicate (thus slowing down play), and simply overpowered for their level when players choose the most optimal monster forms.
Outside of official organized play, Wizards of the Coast could not simply remove polymorph from everyone's books, but with this approach they could at least provide more bounded, balanced alternatives for the use of polymorphing as a buff.