One might reasonably suppose that Paul meant just what any other first-century Pharisee would have meant, the Scriptures were those found in the TANAKH, and perhaps bits of the deuterocanonical writings (Tobit, Judith, Baruch, etc.) as well. This seems like a perfectly acceptable interpretation to me, but it fails to cover the Christian Scriptures, most notably the epistles of Paul.
Another view would be that Paul was prophesying about a canon yet to come, a collection of scriptures which would eventually become the accepted standard throughout the true church. If so, when and where exactly did this collection come into being as a distinct collection of books? Moreover, how long did Christians have to muddle through without a full set of authoritative writings, unadulterated by heretical apocrypha?
Perhaps the Council of Laodicea settled the matter, but it was only a relatively local synod and I doubt Christian apologists would care to argue for the inclusion of the Book of Baruch along with the exclusion of the Apocalypse of John. Perhaps the Council of Trent settled the matter, but I doubt that anyone outside of the Roman tradition really cares to defend that position.
The question remains: where, when, and how was the intended meaning of "all scripture" written in 2 Timothy 3:16 revealed, and to whom? Did Paul know it? Marcion? Origen? Athanasius? Luther? Calvin? Bueller?