I'm planning a trip to Indonesia and was curious if you had any insight on the subject. I've put together a lot of do it yourself adventure travel trips and honestly have never been as stumped as I am by this one. Narrowing down 17,000 islands is a daunting task. Cuba, Nicaragua, Colombia, Egypt etc were all trips that were a piece of cake in comparison.
I have a ticket into Denpasar, Bali where I'm figuring on taking a little time to get organized. From there I'm envisioning two phases. The first to Papua (Indonesian side) looking for barra and maybe freshwater lutjanids (primarily barra). I tracked down a little Youtube footage of some estuary fishing out of Timika in a drainage called Kawar. There are lots of river mouths in the area but this one looks like a shorter system than the rest meaning it doesn't punch into the highlands. As a result, it seems to run clearer (tannin stained) due to the fact it drains low-lying jungle. The info I could gather from the video was limited due to the fact that it was in Japanese and sadly, mines a bit rusty
The second phase would be popping/jigging for GT and doggies. I really want a doggie!!!! The areas that caught my eye were the island chain along the southwest coast of Sumatra (Simeulue, Nias and Mentawi). It looks like there is some tourist infrastructure in the area but it all caters to surfers. Sumba looks like it could have potential and I've also heard Papua mentioned in that light though I have no idea where. I'm guessing the northwest as that area seems to have the best habitat.
I don't need much for amenities. I'm envisioning showing up on a dock with a general idea of where I want to go, charts, printed google earth images and camping gear trying to arrange a multi day boat hire. It's worked for me in the past so I'll roll the dice again. Honestly, I've never felt like I've lost with one of these trips. Sometimes we find fish, sometimes we don't but it's always an amazing experience.
This may be something you don't know much about but if this post jogs any thoughts, insight would be greatly appreciated.