Stroman, Travis, Pompey, Osuna and Sanchez all have 5 years of control and are young guys who would be considered prospects if they weren't already on the MLB roster. If they were still prospects they'd fill out #1-5 on the Jays' minors list. The minors may be relatively barren at this snapshot in time but teams aren't judged by how many MiLB championships they win.
Looking at the Jays' system, yeah it's bottom third. But if you add the guys with 5 years of control who are 25 or under (sorry, Kevin) and did that with every other team in the league I'm sure the Jays would move up into the top half.
The Jays gave up a lot of young pitching depth in 2015, but it's not like I'm losing too much sleep over any individual they traded. Baretto is the only one who really stings and you do that trade 50 times over, even if you have to give up two Barettos and a Lawrie to get it done.