Ok I understand why you state diving Bali was not amazing. (20+ trips to Indonesia, not counting anymore , more than half of them going through and diving Bali)
So in a nutshell :
October to April will be better suited for easternmost Indonesia : Raja Ampat, Ambon, Maluku/Banda
April to almost November is time for Bali & Nusa Tenggara (from Bali to Alor, incl Komodo, Kalimaya, ...), Kalimantan, North Sulawesi (Manado, Bangka, Bunaken, Lembeh) as well as Weh.
Personal favorites : Raja Ampat (best feb-april), Alor, Komodo (best september-november), Ambon & Maluku (best feb-april), Bangka & Lembeh (best April-May), Bali (best End of august-October).