I hope whatever Malaysian FA and Indonesian FA is trying to do, I hope they've learned from the lesson of the Malaysian-Singaporean experiment back in 1994.
Around 1991-93, the cities of Darwin and Perth (both from Australia) applied for admission into the now defunct National Soccer League of Australia. Historically, most clubs in the NSW are from Sydney and Melbourne. To fly from Melbourne to either Perth and Darwin is 5 and 4 hourse respectively. It is cheaper to fly to Manila from Melbourne than it is to Perth. Most Melbourne people fly to Fiji or Vanuatu for vacations because its cheaper than Perth. And most Darwin people fly to Singapore or Bali for vacation - a lot cheaper than flying to Melbourne.
However, the logistics for a Darwin or Perth team is heavy on the financial side - due to the fact that every away game is trully an away game for them (hence, big cost on travel). As oppose to Sydney Croatia vs Sydney Olympic (which is within driving distance from one another).
Then Singapore FA came in with an inter-continental plan in 1993. The plan was to get a "premier league" started in Singapore consisting of Singaporean clubs plus Darwin Cubs FC and Perth Kangaroos FC. The Singaporean competition also included a round robin comps involving Malaysian clubs. For the Australian clubs, it gave them an opportunity to play in front of big crowds when playing in KL or Singapore (ie 15-60,000 crowds).
However, back in Australia, Darwin and Perth can only get crowds between 100-2,000 people. Which was a financial failure for the two clubs. PS: the top football code / type in Australia is Australian Rules Football (which in Perth can get crowds of 50,000 and in Melbourne between 60-99,000).
Perth Kangaroos completed the season unbeaten and Darwin came second (only with 2 losses, both to Perth). Clearly there was a lop-sided standard between the "invited" aussie clubs and the local teams.
This set up only lasted for one season and the Singaporean League collapse soon after (they were re-born as the S-League with only Singaporean teams in it). Apparently, the league was reliant on the money the aussie clubs will rake in - unfortunately, Darwin and Perth were just small time clubs, actually the clubs were reliant on the money the league was suppose to give each club.
The league disbanded in 1995 and so did Darwin and Perth. However, Perth Glory FC was born and entered the NSL. On the disbanded of the NSL, the A-league was created with less clubs (However, Perth Glory retained its place in the A-League).
"Do or do not. There is no try" (Master Yoda)