DP and I are just back from a 19-night intensive (8 cities) tour of Malaysia, Indonesia, and Brunei.
We visited Kuala Lumpur, Ipoh, and Penang/George Town (in Peninsular Malaysia); Surabaya, Yogyakarta, and Jakarta (in Java/Indonesia) and Brunei and Kota Kinabalu (Malaysia) in Borneo. One of us had previously been to Bali, so we left that out. There was of course a whole lot more that we could have done (Sumatra, Sulawesi, Papua, Indonesian Borneo, etc etc).
We made all the arrangements ourselves: hotels (looked up on Booking dot com even if we didn't book much with them), transport (4 trains from the local operators' websites, 4 "internal" flights [internal to the tour, although 3 were international] direct with the airlines after researching on Skyscanner), visits (a mixture of GetYourGuide/Viator and some direct contacts after some Googling), etc.
We ate mostly at local restaurants, including genuine street food places, and didn't get sick or the runs even once. About every third day we would find a slightly more upmarket place if we fancied western-style food or a cocktail.
This pace might not be for everybody, but we travel for food/people/nature more than to visit historical or cultural sights. Last year we did a private tour of India with local drivers and guides, and before that Korea/Japan in a group, and one thing we wanted to change from both was to have fewer visits to "the palace of the 9th emperor" or "the fifth-biggest mosque in the country", which is where the incoming tour companies will tend to take you (also passing by the handmade rug shop).
Anyway, if anyone has been thinking about these countries, feel free to ask me anything.