We must keep in mind that what Paul wrote in 1 Timothy was in regards to Scripture that was written, which was the OT, not the NT. But in all fairness, the NT is also profitable in reproof and teaching.
But the important part of Scripture is that it is literally written through vehicles of God. They are authentically inspired by God. The books canonized were recognized as this, and the books left out were recognized as not being authentically inspired by God. It's possible that those books left out of the Bible are interesting, intelligent, and even have great advice, but if they aren't inspired works of the Holy Spirit, then they cannot be classified as holy, thus aren't valid Scripture.
You're right about the process of writing back then. It was extremely costly to write a book, but costliness doesn't equal holiness. 3 John is only a chapter long, but it is still understood as part of God's Word.
St. Irenaeus, I believe, wasn't the only bishop who had concern for Revelation. A think many had concern with including it. This is why it lead to a council in 397 AD where the bishops had to decide once and for all which books were truly God's Word and which weren't. They came to the sound conclusion that Revelation is and some of the others were not.
Had Revelation been left out, it would mean either it really wasn't inspired by God or it would mean the Holy Spirit didn't work through those who canonized the Bible, thus leaving us with a possibly flawed book.
Do you believe the lost books (Thomas, Judas, Peter, etc.) need to be added?