Hai Lemon,
I was all of these. Maledives: Ari-atoll, Malaysia: Sabah (sipadan etc), Indo: North Sulawesi. And every site has its plus and minus depending on what are you looking for.
Let's start with Maledives: Had Mantas, Whalesharks (but it was octobre), Hammerheads, in generell big staff. Don't expect a lot of macro. Time should be o.k, not the best time (and most expensive). Rain is always possible (even during peak season). Currents.
North Sulawesi: Crittertime in Lembeh (and Bangka)! one word: fabulous! Bunaken is drop off. Nothing too big.
Sabah: Sipadan / Kapalai / Mabul is big and small. Big: Turtles, may be hammers, baracuda (swarm). But have a look at recent reviews here. But for 2 or 3 weeks I would find it too boring. (I was 2 weeks there)
it would be easier to recommend you something, if you could write what are your preference, budget.
In my view Indonesia gives you a huge variety and possibility of a combination. (for ex. Raja and Lembeh, Moluccas etc.).
hope, that helps.
greetings