Hah! Do I.

Breakout:
Black Widow & Daredevil upgrade Combat Expert to Master.
Sentry: Upgrade power traits as per CW writeup.
Human Torch: Add Acrobatics Expert (as per CW writeup).
Black Panther: Add "Anti-Metal Claws" SFX to Wakandan Technology power set (same as the Plunderer's SFX in CW).
Cyclops: Add Psyche Expert (leadership)
Iron Fist: Add Multipower or maybe Burst... his datafile is a bit on the weak side.
Spider-Man: Combine Spider-Powers and Web-Slinging power sets into one, as per the CW writeup (minus the armor power set). Add Multipower SFX. (at that point in time, Spider-Man's web shooters were also a result of his spider-powers. The change also creates a more authentic Spider-Man experience where he isn't using his webbing every panel)
Civil War:
Punisher: upgrade Crime Expert to Master.
Moon Knight: Remove Avatar of Vengeance power set - Moon Knight was very specifically un-powered during Civil War, and in any case hadn't had the "lunar might" effect for years. Maybe keep Enhanced Reflexes (which seems to be on the trainable level, as several non-powered heroes have it) and the non-lunar SFX/Limit. At the very least, remove "Lunar Might" SFX and "Under a Full Moon" Limit.
Cloak: Add Multipower.
Fifty-State:
Black Cat: upgrade Acrobatics to Master. Maybe also upgrade Crime to Master.