The entire polymorph line needs a grounds-up revision. Alter self should stay at 2nd level and let you pick from a fixed list of benefits - movement modes, armor bonus, etc. Polymorph needs to be straight character replacement and should run off of CR rather than HD. Anything which leads to you being a fire giant with spellcasting is inherently broken and can't work. Shapechange should be the same way, except that you keep the round-by-round switching, better size and type options, and the higher CR cap. PAO is fine too with this revision.
Wish needs to lose the XP cost for the lower-tier effects like duplicating spells, wishing for wealth, and gaining inherent bonuses. Cap the value of magic items you can wish for (25k works), and make all items that grant wishes use the 5k XP cost in their pricing. This prevents the wishing for more wishes infinite loop but makes it so that casting wish is actually a viable option.
Make celerity and other effects like it cost your next action rather than dazing you. You still get the "oh shit!" button but now it always comes with a cost, rather than giving people a work-around.
That's my list of most broken spells and their fixes. There are a lot of spells which are underpowered, including most evocations, but that's a much longer list of fixes.