2 Timothy claims that scriptures are "God-breathed". Obviously he was referring to OT scriptures and not the NT
If all scriptures are "God-breathed" (whatever that's supposed to mean) then why are so many scriptures left out of the Bible?
Depends a lot on how you translate that passage. Traditionally, the Christian translators have chosen the biased option of translating 'graphe' as "scripture" -with its implication of 'holy writing', though in fact both words could just as well be translated as "writing".
That would give us "all writing inspired by God". Okay, how do you determine what writing was and is inspired by God?
The glib answer is "what got into the present day Bible" - except a lot of what's in modern Bibles wasn't always there earlier in history. As for restricting "writing inspired by God" to what is now the Old Testament - well what we know as the OT depends on the post-A.D. Masoretic Text, which took quite a while to exist in such a form. The Dead Sea Scrolls tell us that there were a number of versions of the OT available, each version indicating different lines of development.
Even in the earliest versions of the NT we see two synoptic evangelists responding to the earlier text of Mark, and deliberately changing it, because the earlier text does not accord with their idea of Jesus. A typical example of this is Mark stating that "Jesus was angry"*. Matthew and Luke obviously didn't like the implication of this**.
*Mark 1:41
**Nor did many translators. The NIV is honest enough to translate this "Jesus was indignant", though early texts prefer to skew the Greek to mean "Jesus was moved by pity". Since Jesus has just been asked by a leper to be cured, it's easy to see why from the earliest times the text has caused translators and commentators a degree of confusion. After all, Jesus has just informed the assembled crowds, via a text from Isaiah, that he has come to "heal the sick" and all kinds of other wonderful things.