Listed below are all the differences between the main timeline (seasons 1-3) and the timeline without Peter (season 4), arranged by episode and with pictures and timestamps wherever appropriate.
S4E01 - Neither Here Nor There
Olivia was still kidnapped and held in the Redverse while Fauxlivia impersonated her in the Blueverse.
Astrid was a field agent. (Image 1)
Walter was afraid to leave the lab. (Image 2)
John Scott died during the Flight 627 investigation; Walter couldn't save him.
Olivia checked Walter out from the institution.
Image 1: Astrid S4E01 - Neither Here Nor There Timestamp: 14:11Image 2: Walter's room in the lab S4E01 - Neither Here Nor There Timestamp: 42:38
S4E02 - One Night in October
Fauxlivia was still with Frank.
Charlie married Bug Lady from 'Immortality'.
Olivia killed her stepfather as a child.
Alt Broyles was still alive. (Image 1)
Image 1: Alt Broyles S4E02 - One Night in October Timestamp: 27:05
S4E03 - Alone in the World
Monthly evaluations by the director of St. Claire's were a condition for Walter's release from the institution. (Image 1)
Image 1: Walter's evaluations S4E03 - Alone in the World Timestamp: 01:10
S4E04 - Subject 9
Walter hated Nina because he blamed her for breaking the vial with the cure for Peter's disease which ultimately led to the kidnapping and Peter's death.
Olivia ran away from the Cortexiphan trials.
Bell was dead, as far as Walter knew.
Elizabeth committed suicide after both Peters died.
Olivia hadn't heard about/from any of the other Cortexiphan subjects until Cameron James. (Image 1)
Olivia had never heard of Reiden Lake.
Image 1: Cameron James S4E04 - Subject 9 Timestamp: 36:48
S4E05 - Novation
Peter drowned when he and Walter crashed through the ice on Reiden Lake because the Observer never saved him.
Nina raised Olivia and Rachel. Their mother had died, Olivia had killed their abusive stepfather, and Nina stepped in to raise them before they could be put into the foster system. (Image 1)
The team (aside from Peter) don't know about the Observers.
Peter was supposed to die in both universes on that night in 1985 before September's interventions.
Olivia had a horse-riding ribbon.
Image 1: Photo of Olivia in Nina's office S4E05 - Novation Timestamp: 12:29
S4E08 - Back to Where You've Never Been
Olivia had no idea she could cross between universes.
There were "The Amber Riots of '06" in the Redverse.
David Robert Jones is alive. (Image 1)
Image 1: David Robert Jones S4E08 - Back to Where You've Never Been Timestamp: 41:26
S4E16 - Nothing As It Seems
Rachel is still married and has two kids, Ella and Eddie.
S4E17 - Everything in Its Right Place
The USSR still exists in the Redverse. (Image 1)
Image 1: USSR S4E17 - Everything in Its Right Place Timestamp: 04:30
S4E18 - The Consultant
Alt Lincoln's father was still alive. Walternate had mentioned the passing of Alt Lincoln's father in the original timeline. (Image 1)
Image 1: Alt Lincoln's father S4E18 - The Consultant Timestamp: 01:47