Personally I would say that apart from Tulamben, Padang Bai and Nusa Lembongan are really worth it.
I've been disappointed with Menjangan, nice corals but very few fish, whereas on the contrary Gili Tepekong or Gili Mimpang nearby Padang Bai are teeming with fish. There's nothing will find in Pemeuteran or Secret bay you won't find in Tulamben/Seraya/Melasti area
IMO Amed is not worth more than a day dive, esp at Japanese wreck and maybe Pyramids, I found some other dive areas like Jemeluk wall or Bunutan quite tame. You can dive these places from Tulamben.
In my mind, Nusa Penida needs to be dived from Nusa Lembongan because there are more interesting sites to cover than only Crystal bay and Manta point. Toyapakeh for instance is one of the best sites around Bali, you can't miss.
therefre if I had to pick 2 weeks in Bali I would do 7 days in Tulamben area covering Kubu (not so many dives but lots of coral fish unscared by divers) and Amed.
3-4 days in Padang Bai especially for the Jetty, which is simply amazing for weird critters, and the great Gili Tepekong/Gili Mimpang combo.
3-4 days on Nusa Lembongan to cover Nusa Penida dives, it's also convenient to finish for getting back morning at the airport.