Iron monger,Whiplash,Killian,Malekith,Scorch,Blackout,Pierce,Eric Savin,Ellen Brandt,Kurse all died in first appearance and Garret is dead.Zola is a blown up computer.
Red skull is scattered along ygdrysil.
Winter soldier,Deathlok are reformed.
Blizzard,Graviton,Leader haven't become villians yet(but are all trapped in one way or another).
Abomination,Batroc,Hammer,Trevor Slattery(or being beaten up by the real mandarin) is in jail.
Crossbones is in intensive care.
Strucker,Thanos are lurking behind the shadows.
Loki,probably killed Odin,and took over Asgard.