Mr. Blues, we flew from Jakarta to Sorong (via Makkasar) on Express Air in October. Express Air seemed fine: reasonably new Boeing 373, departed and arrived more or less on time, no trouble with out checked bags. Food served on the flight was a little funky but at least some of it was edible (this is what I expect on domestic Indonesian flights). All in all, no problems. We flew Express Air because our dive op strongly recommended them (and because the schedule worked for us).
Coming back, we flew on Lion Air from Sorong to Jogjakarta (via Ambon and Surabaya). Although I had previously flown on Lion Air a couple of time and found them to be fairly reliable, things didn't work out well for us this time: the first flight was an hour late, the second flight was later still, and that meant we missed our connecting flight from Surabaya to Jogja. Lion Air did put us on a later flight that night, which was probably OK - although this happened to take place right as Mt. Merapi was having a major eruption, which caused a cascade of problems for us (not the airline's fault or anyone else's, and hopefully not a consideration for you).
The Indonesian travel agent we used (and EVERYONE else) warned us away from Merpati. I'd consider them a last resort.
Although Express Air's website is broken and only partially functional, we found their flights to be reliable enough, and the folks at our resort urged us to use them, at least for the inbound flight.
Hope that helps. And good luck!
