Other teams likely want the best guys in your system. How often would you be an a position to trade a highly regarded prospect with big market value that you're pretty sure will bust? If Toronto, for example, had the payroll restrictions of Cleveland or TB, Syndergaard, d'Arnaud, Desclafani, Hechavarria, and Dyson putting up tons of wins for league min on other teams would have absolutely crippled the team's chances to compete.
And evaluation is hard. Toronto drafted Sanchez and Syndergaard, and still preferred Sanchez to Syndergaard at the time of the Dickey trade. They had Yan Gomes in the system for half a decade and didn't think he could catch. They had JPA in the system for half a decade and thought he could catch. Keeping talented minor leaguers rather than selling them for expensive vets is really the only way a team with a below-average payroll can hope to string together playoff seasons.