Don't forget he messed with Peter, too (and considering the rather prominent focus we're seeing on the Peter/MJ relationship and the supernatural aspects coming in with the Centidemon, I'm beginning to think they might actually be doing something with it). Are we gonna see the 4 Spider-Men of the Apocalypse? (5 if you count Flash-as-Venom).
Or they're building up to an event where he's going to play a big role. He's got the Squadron Supreme is his pocket, a hold on some of the Champions, plus the Circle of Four (while I don't know what happened to that incarnation of Ghost Rider, X-23 is around and kicking, and Flash & Ross are both dead - the latter explicitly identified as being in hell - so maybe he's going to cash in his chips). Maybe he's getting the pieces into place for his big play.