Bunaken has very good diving but not much else to do in Manado or North Sulawesi except for day trips to Lake Tondano or Tangkoko Park. Bali has excellent diving: from Mola-Molas in Nusa Penida, sharks in Padang Bai and critters at Secret Bay to good walls at Menjangan, plus one of the best shore/wreck dives in the world at Tulamben. The possibilities for sight seeing, shopping, white water rafting etc. at Bali are much, much better. Prices are comparable, somewhat lower in Bali
The best places in Indonesia are Komodo and Raja Ampat accesible thru liveaboards, ditto for Misool (great for critters). Wakatobi resort is overrated and overpriced. Lembeh strait is a shadow of its former glory due to resort proliferation and diver pressure.