[{Id:123,data:{A:3,B:4,C:34,D:45,E:4}},{Id:123,data:{A:5,E:33}},{Id:123,data:{B:499,C:24,E:39}},{Id:123,data:{A:63,B:34,C:534,D:845,E:84}},{Id:123,data:{E:4}}]

db.collection.aggregate([{$group:{_id:"$Id",A:{$push:"$data.A"},B:{$push:"$data.B"},C:{$push:"$data.C"},D:{$push:"$data.D"},E:{$push:"$data.E"}}}])