Database
[{Skus:[{skuId:"Boo",name:"Foo",color:"red",size:"small"},{skuId:"Moo",name:"Foo",color:"red",size:"large"},{skuId:"Moo",name:"Foo",color:"yellow",size:"small"},{skuId:"Moo",name:"Foo",color:"red",size:"medium"}]}]
Query
db.collection.aggregate([{"$unwind":"$Skus"},{"$group":{"_id":"$Skus.color","size":{"$addToSet":"$Skus.size"}}},{"$replaceRoot":{"newRoot":{"$arrayToObject":[[{"k":"$_id","v":"$size"}]]}}}])