EDIT: I actually found a few more!
It shows Tepig growing up with the rest of the family.
Plusle and Minun make a rainbow.
Pulsle and Minun are in the same place, different shots.
Charmeleon and Swablu that you mentioned.
Natu & Bouffalant that you mentioned.
Trubbish, Phione & Empoleon that you mentioned.