Between allepey and kumarakom you can visit one.. Allepey has great houseboat facilities.. wheras kumarakom is a little less commercial.
you can check my trip for munnar allepey
Kochi -> kumarakom -> alleppey -> munnar -> kanyakumari -> rameswaram -> bangalore u can skip kumarakom and spend 1 day each in alleppey,kanyakumari,ramesawaram and 2 days in munnar.