How do you know it’s PITA if you have never been there? I’ve been to Alor, Raja Ampat and Maratua Atoll and I can compare my travel experience to those places. Flight to Alor would be the worst among the 3 destinations.
I don’t know how you come up with $700 roundtrip Jakarta-Berau. Did you check Sriwijaya Air? They are pretty good airlines. I have used them flying from Jakarta to Bali, Sorong, Berau several times in the past (to Sorong may be 4 times) and will be to Maumere this coming September. I haven’t missed / cancelled a flight with them, yet (knock on wood). I have a flight cancelled by Garuda once. That’s a PITA.
I just went to Sriwijaya Air website and try booking a roundtrip flight for next month at a reasonable schedule time, (not at wee hours, which would be ~$100 cheaper) and get about $490 for roundtrip Jakarta- Berau with a stop in Balikpapan, as shown below.
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As fas as the diving consistency, it depends on the time of the year, the same as any other sites, for example, Raja Ampat is better to be visited from November to March.
Maratua Atoll may not have the bio diversity of Raja Ampat, however if you want to see the big fish, like the schooling of barracuda as you see in Sipadan, Maratua Atoll is just as good as Sipadan, as you see in the videos I posted earlier. There are dive spots in Maratua Atoll where you can see Thresher sharks too. That’s what I want to check it out on my next visit to Maratua Atoll.