Very true, on paper the AURI had a much larger and more powerful fleet than the PAF. But unlike the PAF, who had access to the American support infrastructure at Clark, the AURI had great problems mantaining its diverse Soviet supplied aircraft fleet, a problem only made worse after 1965 when spares all but dried up. The decline of the PAF only started in the early 1980's.
Yes, the infrastructure for hard skill supposed to be prepared later on, since at the 60's the focus was for training to fly and maintain the fleet, whille the facility for support was supposed to be in the late 60's. By the time Soekarno's fall, there are more than 5000 Indonesian students in Russia and Eastern Europe whille around 2000 or more in China. Those students study and train the hard science and advance technical to prepared for 'strategic' industry that the Russian and the Eastern Block promissed Soekarno to help build by late 60's and early 70's.
Incidently those infrastructure included Nuclear reactor that design to be Plutonium breeder, supposed to be located in Serpong. This was later on by the time of Soeharto's being change as compensation by the west to nuclear research facility (including 30 MW research reactor) in the same location.
In sense, SEA will be in much different condition if in the 70's Soekarno still in the helm of Indonesia. Soekarno have different perpective on the Industry compared to Soeharto. Whille Soeharto aimed for Industry that can produced something that can be exported, Soekarno aimed for basic Industry that can be developed for Heavy and Strategic Industry (and he does not cared for Export or strengthening Private sector in that matter). He's revolutionaries like Mao's, and just like Mao's he's looking for something grandeur that can be sold as prideness to the people and not something that can 'just' feed the people. Afterall that's the shortness of most Revolutioners in the world.
BTW, some US historian claimed that US support for Permesta was seen by Kennedy's administrations as mistakes by then Eishenhower administrations. Kennedy's thus try to coerce Soekarno including giving him a Squadron of C-130B (thus make TNI-AU as the first Asian nation that had C-130) as compensations for what US support to Permesta. In sense it's being given also to get Allan Pope released.
Khruschev then after that besides giving Soekarno's more Fighters, he also give him a Squadron of AN-12, just to show Soekarno that Sovyet got something that can match C-130. BTW, when Soeharto send Ali Moertopo (his right hand man) to KL, to fix the fence after KONFRONTASI, he's flying with AN-12.
Anyway it's a little bit out of topic of Indonesian Army