I had a problem with discovering my great grandfather as my grandfather was illegitimate.
My sister and I started searching when I was 8.I finally discovered who he was 4-5 years ago so it took about 65 years!
That's amazing! Thanks for sharing that. I think there are ways forward for us too, but it will be difficult.
(1) Civil registration records aren't very helpful, but I notice that there are generally more civil registration birth records than there are baptism records on Ancestry. Some people didn't have their child baptised, some church records have been lost, and of course there were many different churches. Most Welsh records on Ancestry seem to be Anglican, but when John married in Australia it was in a "Primitive Methodist" church. So was that his religion in Wales, and are those records in Ancestry? I will have to check that out. But it may be that the records are simply no longer in existence.
(2) Sometimes the only way to make progress is to buy certificates, which may have more information than is available online. But buying dozens of certificates can be costly! (In Australia they are typically $20 or more, while in Scotland they are only a few dollars.) But I need to look at this option.
(3) Finally there is the old way of going to churches and historical societies in Wales to look at actual records. I'm unable to do that myself, but perhaps we can pay someone to do it. (My great grandmother and my grandmother's birth in Australia was found that way. The online records didn't allow searching on the exact date, but looking at the actual record book at the local council allowed my grandmother's birthdate to be examined.)
So I will have to either wait to see if DNA reveals John's parents, or put in a lot more work, as you did.