The following is a list of Pokemon whose evolution methods are different from the base game:
Gurdurr to Conkeldurr: Lv40
Boldore to Gigalith: Lv40
Haunter to Gengar: Lv40
Yanma to Yanmega: Friendly Evo
Mantyke to Mantine: Friendly Evo (NITE)
Cottonee to Whimsicott: Leaf Stone
Petilil to Lilligant: Leaf Stone
Eevee to Leafeon: Leaf Stone
Roselia to Roserade: Leaf Stone
Lampent to Chandelure: Fire Stone
Eevee to Glaceon: Ice Stone
Piloswine to Mamoswine: Ice Stone
Karrablast to Escavalier: Shell Stone
Shelmet to Accelgor: Shell Stone
Onix to Steelix: LvUp w Metal Coat
Nosepass to Probopass: LvUp w Metal Coat
Magneton to Magnezone: LvUp w Metal Coat
Electabuzz to Electivire: LvUp w Electrizer
Magmar to Magmortar: LvUp w Magmarizer
Seadra to Kingdra: LvUp w Dragon Scale
Eevee to Sylveon: LvUp w Magic Ribbon