Twilight Sparkle as Phineas (both are the main characters)

Spike as Ferb (both have green hair and speak with accents)

Big Macintosh as Lawrence

Princess Celestia as Linda

Fluttershy as Baljeet (both can be shy at times)

Owlowiscious as Perry (Owlowiscious and Perry are good pets to Twilight and Phineas)

Rainbow Dash as Stacy

Rarity as Isabella (both are pretty girls)

Pinkie Pie as Jeremy

Starlight Glimmer as Irving

Princess Cadance as Candace (both names start with C and end with E)

Derpy Hooves as Vanessa

The Great and Powerful Trixie as Ginger

Granny Smith as Albert

Nightmare Moon as Professor Poofenplotz 

Discord as Doofenshmirtz (both names start with a D and they're the male villains)

Dr Hooves as Major Monogram

Applejack as Buford (both are hard workers)

Princess Luna as Betty Jo

Two Changelings as Thaddeus and Thor