I had two months away two years ago , spent four weeks in Indonesia , then a week in Cambodia and the plan was 3 weeks in the Philippines....when it rained and rained , so I spent the last 8 days in Thailand.
We did a liveaboard to Raja Ampat the first month which was awesome ...in summer Komodo is at it's best, so I would really recommend you fo there , plus a week in the islands off Bali plus a week in Sulawesi. There are plenty of lower budget liveaboards or back backer budget resorts. Then head to the Philippines , via Luang Prabang in Laos or Siem Reap in Cambodia. Six weeks goes quickly and moving between countries quickly adds up.