This is such a hard question since pretty much all of the Johto Pokemon are cute. :o
However, I would personally say Teddiursa, Mareep, Hoothoot, Sentret, Girafarig, Corsola, Togetic, Igglybuff, Cleffa, Smoochum, Magby, Marill, Misdreavus, Dunsparce, Yanma, Pichu, and Hoppip are all really cute, with even more Gen2 Pokemon also being cute.