Why don't you try using Garuda Indonesia (GA)? As I have said in my posting on other topic, GA have improved much in the past 5 years, and I have experienced it too... When I went to AMS in 1994 using GA, they stopped over at CDG, although I'm not sure whether they are still serving CDG, since the Asian economic crisis forced GA to closed many of its routes.
For your domestic flights, nowadays there many domestic airlines in Indonesia. There are the old players such as Merpati, Bouraq, Mandala, and of course, Garuda. And there are also some new players (due to the deregulation), like AWAir, Lion, Bayu. Each has a unique market segment, in the sense that one airline is more favourable in one route, whereas in another route, another airlines is more favourable. If you like to try new airlines, this might be a good chance to do so.
Garuda only serve major cities in Indonesia, since they have transferred most of the domestic routes to their sister company, Merpati, so that GA can focus more on International routes.
Merpati is the biggest domestic carrier, in term of routes and fleet size. Its routes cover all Indonesia, even the remote jungles in Papua.
BTW, if you happen to come to Jakarta in the end of June-early July, I think we can meet.....since I will come to Jakarta to visit my parents.