Is this report for real? I am very surprised. I have been living on and off in Indonesia for 6 years now. Travel quite frequently to Europe, many times every year. Terminal 2 may not look very attractive but I have never had to spend too long a time for security, check-in and immigration. Of all the flights I have taken (which are many) I only remember one which was a little bit late. Usually they are pretty much on time, no matter if it is Garuda, the Gulf airlines, KLM or others. As for arriving, only one time have I had to wait for a long time for my luggage, around one hour. Usually it is only a few minutes wait after immigration. And my bags have always arrived without anything being stolen from them.
As for the Air traffic control, they usually make us do one or two holdings north of Jakarta but never have I experienced more than two. Last year I read a report that they needed 2000 new controllers, preferably "yesterday". I think they are doing a decent job with what they have (I know a bit about this being a former controller myself).
Maybe I am just lucky but it seems to me that this airport is not too bad. The only thing to complain about in my view is the lack of a well stocked bar.