I've seen dozens of houserules about the Shapechange series of issues (not to mention the multiple ways WotC tried to fix it). My personal method of dealing with it at the time was to attack if through the Natural Spell feat. I came up with two similar methods.
Option 1 is to just remove Natural Spell altogether. When you remove the ability to cast in polymorphed form, it forces the character to change back to normal form a lot more often, and puts an immediate end to the worst abuses of characters walking around in alternate firm 24/7.
Option 2 is to make Natural Spell a Metamagic feat instead of a general feat. This means the character has to decide when they prepare spells if the spell will be cast in alternate form or in normal form. This puts a much larger focus on the strategy of spell prep and resource management.
Neither of these options are complete fixes, but I find they are the simplest changes with the biggest effect. While I think Option 1 is cleaner, it comes across to players as a straight nerf. Option 2 is a more complicated, but makes players feel like they have more control.
Why not just use Option 1, and change the spell to require constant focus and concentration to maintain the form? Cuts out the ability to cast spells while polymorphed, gives a grounded explanation (because maintaining the form of a dragon requires a lot of mental effort), and doesn't come across as quite nerfed?
I therefore require a player who could shapechange (or summon creatures) to have already prepared an adjusted character sheet (or stat block) for each and every form that they wish to assume and further require that the form be one the character is familiar with through study or experience. They can't just flip through a monster manual and pick out forms. They either have to be acquainted with the creature from personal experience or find a suitable library for conducting research and spend time studying and researching forms. Unpracticed and ad hoc forms would generally require a spellcraft check to get "right" with failure indicating penalties to effective dexterity and unusual appearance that would readily cause anyone actually familiar with the form to recognize it as false and assumed. And again, I wouldn't even allow it unless the player can immediately provide the adjusted character sheet.
This is also a solution that can be used with Option 1 above, and you could go further and require the player who wants to be a shapechanging archmage to have skills in Knowledge (Dungeoneering) or other appropriate categories, and each monster would have to be researched (leading to the wizard's notebook becoming something of a plot device itself as such notes would be highly sought by other wizards...) and studied for a minimum period of time/a minimum number of successful knowledge checks made.
"Natural Spell" was a mistake, as it produced a situation where the Druid was a better fighter than the fighter while simultaneously being competitive with a Cleric as a healer and with a Wizard as a general caster. I don't allow the feat, as it was both overpowered and therefore compulsory.
You'll notice if you read carefully I dropped "Druid" as a class altogether in favor of a Shaman class based off the Green Ronin class, but that's a different discussion. It's still possible to build a Druid in my game, by playing a Shaman and selecting the appropriate totems, but the class is generally less versatile. You'll notice from above "Wild Shape" isn't a class feature but a spell.
Making "Natural Spell" into a metamagic feat isn't required or even helpful, as there are already things like "Silent Spell" that would let you cast a spell in animal form if it only had a verbal component, etc. Just pay attention to those components and remember they are a balancing factor in being a spellcaster. Spellcasters should not outshine non-casters, and it is a mistake to make it easy for them to do so in the name of making playing a spellcaster less situational or complex. You want an easy class to play, play a (well designed) fighter class.
I'm actually planning on doing something similar within my own version of 3.5e that I'm tweaking specifically for my campaign world (a low-magic campaign), and using books like,
The Practical Enchanter and other books that introduce folk magic and witchcraft in a way that doesn't involve use of spells and the like. That, in turn, provides a way for characters to get healing without requiring the landscape be dripping in magic. It also sets up conflicts with locals who now have a ready source of superstition and regions where witchcraft and folk magic is outlawed entirely.
Also, why not build out the subskills more? Has anyone tried expanding skill lists and/or expanding their subskill uses? I'm putting together a list of tweaked Skills to be added to the SRD skills (mostly Craft, Knowledge and Profession with a few others not in those categories) specifically so that players have more options within their own skill sets to do the stuff normally done by magic, or at least, able to be accomplished without magic. I'm drawing from the
Ultimate Game Designer's Companion, Experts v.3.5, Races of the Dragon (for mining rules under Profession, so far),
101 New Skill Uses by Rite Publishing, and other more obscure 3.5e third-party supplements, and putting them together in a list to offer players that is (hopefully) far superior to the standard skill list. Doing this will, I hope, encourage players to get more creative with their skill checks and use them more than falling back on magic.
