Politically correct ways of saying someone "doesn't have it altogether":

He never had a full box of crayons as a kid.
A few clowns short of a circus.
A few fries short of a Happy Meal.
An experiment in Artificial Stupidity.
A few beers short of a six-pack.
Dumber than a box of hair.
A few peas short of a casserole.
Doesn't have all his corn flakes in one box.
The wheel's spinning, but the hamster's dead.
One fruit loop shy of a bowl.
One taco short of a combination plate.
A few feathers short of a whole duck.
All foam, no beer. 
The cheese slid off his cracker
Body by Fisher, Brains by Mattel.
Has an IQ of 2, but it takes 3 to grunt.
Warning:  Objects dumber than they appear.
Couldn't pour water out of a boot with instructions on the heel.
He fell out of the Stupid tree and hit every branch along the way. 
An intellect rivaled only by garden tools.
As smart as bait.
Chimney's clogged.
Doesn't have all his dogs on one leash.
Doesn't know much but leads the league in nostril hair.
Elevator doesn't go all the way up to the top floor.
Forgot to pay his brain bill.
Her sewing machines out of thread.
His antenna doesn't pick up all the channels.
His belt doesn't go thru all the loops.
If he had another brain it would be lonely.
Missing a few buttons on his remote control.
No grain in the silo.
Proof that evolution CAN go in reverse.
Receiver is off the hook.
Several nuts short of a full pouch.
Skylight leaks a little.
Slinky's  kinked.
Surfing in Nebraska
Too much yardage between the goal posts.

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