I am very sure the governing body of Indonesia is very similar to Malaysia. Got its own problems and bureaucratic.
The main difference is between the Indonesian and Malaysian players is one thing : their attitude. In the past, I would agree that Malaysian players can never be compared with the Indons because the latter are faster, fitter and somehow they have the right technique to execute the right shots. In modern era, it's no longer an excuse. There's no such thing as Indonesian secret shots or smashes. Everything can be studied, analysed and reproduced thanks to technology and sports science. Indonesian players are not special anymore. Any random player with the right training and preparation can beat them.
In the past, I would think Taufik is an impossible player to beat. Once we enter the modern era of technology, Taufik is just another player that can be beaten by any random top 50 player.
Now what separates Indonesians from Malaysians is their hunger for success. They train and compete patiently until they no longer have the ability and stamina anymore to compete. I would say the most patient award should go to Hendra Setiawan. That guy is literally the silent collector of trophies. Sure he may not be consistent with a lot of rollercoaster rides but he carries on competing and training until he wins. And his most recent victory is finally getting hands of the Thomas Cup. Of course other indonesians like Lilyana and Greysiaa are also comparable in terms of patience.
But what about Malaysian players? Put aside BAM mismanagement and short-sighted goals, the players themselves are culturally different in terms of their thinking to Indonesians. Perhaps owing the bad state of Malaysian education system or even society, Malaysian players simply fail to see the bigger the picture and do not have the patience to succeed. Once fallen, most of them cannot bounce back from failure and automatically career over. This is really the case for most Malaysian players. Liew Daren's career is more or less over when he flopped in the Thomas Cup and the same goes to Chong Wei Feng when he got a master class beating by Momota. These are potential players that could go far in terms of their skills but they do not have the right attitude to bounce back and recover. Another infamous story is Kuan Beng Hong. That one is a serious flop story. Totally unprepared to prove his worth and one crucial defeat completely led to self-destruction.
Lee Chong Wei is an exception with his biggest flaw in his career is being too arrogant and overconfident with himself and allowing his rivals/enemies to analyse him like an open book. What is the point of going all out winning all these series titles and beating your opponents hands down only to fail at the crucial big tournaments ? It's sign of failure to see the bigger picture.
Until the national team has a new set of badminton players who are critical thinkers, hard working and of course very talented, Malaysia will be seen as country that fails to win big tournaments which is a sad revelation when Malaysia is already falling behind in many aspects of the world due to reasons which we all rather not discuss.