I've flown both airlines and had no problems. Have flown Lion from Singapore to Sumatra and onto Makassar, Sulawasi; from Sulawesi to Balikpapan, Kalimantan; from Lombok to Surabaya and then to Singapore; and for getting back and forth between Lombok and Bali numerous times. I've also used Garuda internationally (from California to Jakarta) as well as for domestic routes. Just bring your own snacks. (The food leaves something to be desired, and I have an adventurous palate with a penchant for street vendors.)
Both airlines were certainly more reliable than Merpati, which I've also flown a ton out of lack of a better option in the "backwaters."
Here are two Merpati tales, should you have time:
1. Once in Flores, Merpati shut down all flights out of Maumere (in the northeastern part of the island) due to an active volcano that was belching up ash all over the town. Fair enough. That's dangerous. I'd seen the sucker shooting up a white column while going down for a dive. But we had called the Merpati office the day after the ash starting coming out to confirm our tickets, as instructed, and Merpati confirmed our reservation without a problem. I know there was no language barrier because the owner of our guesthouse got on the phone to make sure.
Now, in Flores, though not everywhere, Merpati agents work as a sort of franchise, so you have to book and pay for the ticket in the town that you are flying from. (A Merpati agent won't even call all another Merpati agent in a different city. You make and pay for the call yourself.)
So two days after the volcano incident and the day before our flight we went into town to pay for the ticket. It was then that the Merpati agent informed us that they had cancelled all flights starting from the day the volcano started coughing through the coming week.
We ended up hiring a car and driver to take us to Ende in the middle of the night. Got up at the crack of dawn and lurked at the airline office until someone showed up to work and got two of the last tickets, as everyone else in the area had been rerouted by the volcano too. In the end, we could only get to Bali via Sumbawa. This meant we had to buy another ticket to fly to Mataram, Lombok so that we could catch our flight to Singapore, in order to catch our flight back to NYC.
2. On another occasion, I took Merpati from Manado to Gorontalo in order to catch the overnight ferry to the Togeans. We got on the plane, which had foldable school-bus style seats, and suddenly felt a poke from below. Turns out we were sitting on a Leatherman. Who knows if it belonged to the last passenger (how did that get past security?) or whether it was being used to fix the plane.
The plane took off, but the cockpit door was never closed, so I was able to witness the pilot's activiites. About 20 minutes into our flight the captain spread the comic strip section of a newspaper over the entire window of the cockpit, carefully tucking in the corners to make the paper stay. This blocked the sun's glare. However, it also meant the pilot couldn't see. Now, I promise you there was no radar on that plane, and the newspaper stayed up until the last 10 minutes of the flight when we were preparing to land! No joke.
