Mickey Mouse/Batman

Heroes
Mickey Mouse - Bruce Wayne/Batman (Both the main stars)

Yen Sid - Commisioner James Gordon

Goofy - Alfred Pennyworth

Launchpad McQuack - Detective Harvey Bullock (I'm running out of choices)

Donald Duck - Dick Grayson/Robin

Sylvia Marpole - Barbara Gordon/Batgirl

Pluto - Terry McGinnis/Batman Beyond

Jose Carica - Officer Renee Montoya

Chief O'Hara - Mayor Hamilton Hill

Panchito Pistoles - Zatanna

Villains
Pete - The Joker (Both the main villians)

Mortimer Mouse - Oswald Chesterfield Cobblepot/the Penguin

Minnie Mouse - Selina Kyle/Catwoman (Both Mickey and Batman's girlfriends)

Ludwig Von Drake - Edward Nygma/the Riddler

The Troubadour - Dr. Victor Fries/Mr. Freeze

Chip - Harvey Dent/Two-Face

Clarabelle Cow - Dr. Pamela Lillian Isley/Poison Ivy

Daisy Duck - Dr. Harleen Quinzel/Harley Quinn (Both love to Donald and Robin)

Horace Horsecollar - Dr. Johnathan Crane/the Scarecrow

Dale - Waylon Jones/Killer Croc

Doctor Frankenollie - Matt Hagen/Clayface

Kat Nipp - Ra's al Ghul

Baby Shelby - Mary Dahl/Baby Doll