In the 60's, Indonesian Navy operated 10-12 Whiskey class submarine. Besides the submarines, USSR also provided Indonesia with basic supporting Infrastructure (on sea and land), from submarine tender ship, to submarine berthing infrastructure etc. On top of that a very friendly pricing spare parts supply.
By the early 70's those dozen submarine already decreased only to 4 operational and by mid 70's only 2. Despite that Whiskey class is not a very complex and expensive submarine to maintain, however for a small navy or a third world nation navy it's an expensive hardware to maintain. This with the fact that TNI-AL already had considerable submarine infrastructure for Southeast Asia standard at that time (well the only one in the region at the 70's)
It requires special technical skill, different set of crews training and preparations (you can't simply transferred surface ship crew, and conduct little bit training and hoping them to be capable submarine crews right away). In fact just last week, two TNI-AL crew dies on submarine rescue training exercises. Just to show, even with more than 40 years experiences on submarine operations, TNI-AL still need to learn a lot to keep maintain and developing their submarine proficiencies.
This does not mean that a Navy without previous experience on submarine operations can't operate Submarine. Singapore and Malaysia show they can do that, however with a long time preparation before and 'a lot of' Investment. When talking Investment, this means not just buying and maintaining the submarine, but also preparing everything else in support the submarine operations.
The 2nd-hand German subs that Thailand were considering were said to be 35 year old but said to only last another 6-7 years more.
Indonesian Tjakra and Nenggala, both over 30 years old, but after huge modification, overhaul, and upgrading with Daewoo, they can operate up to end of next decade if need be. This is the third overhaul being conducted to both submarines, First in Manfacturer facility in Germany, then in PAL Facility in Surabaya, and lastly in Daewoo facility. Despite PAL already able to conduct 209 overhaul in Surabaya, the last overhaul choosed being conducted with Daewoo, since Daewoo is license to build newer versions of 209 (Changbogo), thus can provide the upgrade for Indonesian 209 with some elements of Changbogo technology.
The overall 'real' price on upgrading those two 209, I've been told actually closed to having 1 brand new 209. The Navy choose to do that so they can have 5 (2 old-upgrade 209 and 3 brand new 209) subs by second half of this decade.
All this show how expensive, and complex issues facing a Navy when operating submarine, even a Litoral-Green water subs like 209. TNI-AL choose not having Kilo, but another 209 is also related with the complexity on maintaing and operating submarines.
Besides, Japanese already invest so much and put much of their own advance technology on their submarine. It's too early to tell that Japanese will provide their Subs to Philipine Navy. Even Australia (RAN) interest with Soryu and their close relationship with both Japan and US, will not guarantee automatically that Japan will share much of their Soryu Technology with Australia. Much must be seen.