We've done our own air for years, although I am using air/sea with RCI for my little jaunt on the Sovereign this month. In this case it was a wash with doing my own, and the included transfers made it an obvious choice. I was a bit surprised since, as you note, cruise line air has really been a poor choice for most cruises over the past several years.
I remember a repo cruise we did on the Song Of America in 1993. 4 nights from San Juan to Miami, and RCI had $100 per person air - ATL to SJU, and then MIA to ATL. The cruise was $299 per person for us, and then I won $800 in the ship's casino on a slot machine. The cruise with air was free. Those deals are long gone.
Charter air, I predict, will make a comeback as Hank suggests. It may be quite common for distant cruises, as the only way a cruise line can sell out a cruise.
There will certainly be a lot of airplanes available for charter airlines to lease.