Quoting wanderitch
I heard its expensive, and just a general preference of other south east asian destinations. It doesn't seem to anybodies favourite. 
When you factor in the price of a plane ticket to Indonesia is that place any more expensive than Malaysia?
Last November I took a train down to Hat Yai and then went over to Malaysia, the train was pretty cheap. Malaysia was not that expensive. The train goes all the way to Butterworth (near Penang) and then on to KL. You can also go on to Singapore by train if you want. Singapore definitely is more expensive than Malaysia.
Up to you, but if you want to save money Malaysia might be no worse without paying for a plane ride too!
Last time I was in Indonesia was around 11 years ago. Stopped in Bali and then flew down to Sumbawa Besar (Merapati Airlines) where I worked on a charity project for Earthwatch. There are some recent terrorist warnings concerning Indonesia, here is one from the US.
http://travel.state.gov/travel/cis_pa_tw/tw/tw_918.html
There have been several since the terrorists blew up the bar.
Good luck.

