Spells that need fixing (for their level, and for diverse reasons) in my book include, in alphabetical order:
Alter Self [fix: remove the natural armor clause]
Astral Projection [fix: spell ends if the recipient leaves the Astral Plane by any means; OR doesn't make copies of worn and carried items]
Black Tentacles [fix: allow a Reflex save to leave the area un-grappled]
Comprehend Languages [fix: gives a set bonus of +10 to Decipher Script skills instead of auto-deciphering]
Divine Power [fix: remove the ability to cast spells while under the effect of Divine Power]
Enlarge Person [fix: reduce duration to 1 rd/CL, and move to 3rd level]
Entangle [fix: reduce radius to 10'; OR move to 3rd level]
Freedom of Movement [fix: move to 6th level]
Gate [fix: delete the clause "In the case of a single creature, you can control it if its HD do not exceed twice your caster level."]
Glitterdust [fix: "Spell Resistance: Yes (blinding only)"]
Knock [fix: adds a set +10 bonus to Open Lock checks]
Mage's/Mordenkainen's Disjunction [fix: does not permanently destroy magic items, but does suppress them for CL rounds]
Magic Circle vs. Evil/etc. [fix: see Protection from Evil, and move to 5th level]
Mind Blank [fix: reduce duration to 10 min/CL]
Mirror Image [fix: move to 3rd level]
Planar Binding line [fix: don't set a HD cap, set a CR cap instead; or use Summon Monster-like tables for call-able creatures]
Protection from Evil/etc. [fix: only protects from possession and mind control originating from creatures of the warded-against alignment, and move to 3rd level]
Polymorph [fix: only allow polymorph subschool spells. Sure, this has been said by WotC, but many groups still allow Polymorph all the same]
Polymorph any Object [fix: there is no fix. This spell must go]
Resist Energy [fix: do not increase the energy resistance at higher CLs]
Shapechange [fix: remove the ability to use the spell-like and supernatural abilities of a creature you shapechange into, and introduce a clause stating that you cannot use any natural spellcasting the creature you shapechange into might have (such as a Planetar's Cleric spellcasting)]
Wall of Stone/Iron [fix: these spells need a duration other than instantaneous, I'm open to suggestions]
What do you think?