- Don't let the druid be good at everything. As Veekie mentioned, the PHB2 Shapeshift variant cuts it down quite a bit. Granted, I think it could have been implemented better, but it is a quick and dirty fix.
- Cut certain spells or mechanics from the game entirely. Polymorph is too hard to get working in its current version. It needs to be cut or replaced. Planar Binding and Gate allow casters to gain access to things way above what they normally could. The trope of demon-binding is a really good one from a thematic perspective, but it needs to be reigned in from a mechanical perspective.
I would argue that instead of nerfing the Druid with the Shapeshift variant, the same thing that should be done with the Wizard should be done to it, split it into different classes. The classes would likely be an elemental focused caster, a shapeshifter (in the vain of Master of Many Forms), and an animal companion focused class (which would subsume much of the Ranger class including its name and minus the spellcasting).
I also think that a similar, though more extreme, thing should be done spells like Polymorph and generic summoning spells. Instead of the ridiculous variability there is now, one form/one summon should equal one spell. So if you wanted a new form or summon, you would have to learn a new spell entirely. For example, if you wanted to become a young adult male red dragon missing one fore claw, you would have to learn a variant of Form of X, focused on the form (with a level that changed based on the power of that form).
With Polymorph gone, the shapeshifter would move in to fill the character archetype of its name sake but with that being its only thing instead of one thing in many.