You are correct that Joseph was not in Philly in 2015 and that concussions kept him from playing very much in 2013-2015, which is why it strikes me as strange that you use his minor league stats to justify such a pessimistic view of Joseph. His 2016 is not SSS. Over 300 MLB AB and about 100 really excellent AAA AB, so that's just over 400 AB. That's quite a decent sample size.
Joseph's minor league results really aren't as bad as you make them out to be, especially because he move through the minors so fast and was young for the leagues he played in. You have to give him credit for age vs level on the stats, where you just quote his minor league career averages.
He started in the SAL at age 18. How many players do the Phillies send to Lakewood at age 18? He also suffered a concussion that year, which certainly didn't help his stats. This was his lowest OPS season with significant AB. He only posted a .691 OPS but did make the All-Star team. In 2011, at age 19, he was in high-A and boosted his OPS to .788. We got him as a AA player in 2012 at age 20. I couldn't find the reference, but remember reading that he had another concussion while with the Giants' AA., where he posted a .704 OPS before finishing the season in Reading with a .747 OPS. His Phillies career was then marred by both further concussions and wrist surgery, effectively negating his 2013-2015 stats. I'll note that even as an 18-year old in the SAL league, Tommy showed in-game, not just the raw power you credit him with, hitting 16 HR in 436 AB.
I agree with CD. Joseph is finally healthy again for the first time since 2012 and last year showed what scouts always expected of him, including the Phillies scouts who recommended building the Pence deal around him. You keep using his minor league stats to cast doubt upon his 2016 stats but, in addition to seeing his pre-2016 minor league stats as largely irrelevant in predicting 2017 major league performance for a guy with 300 MLB and 100 AAA 2016 stats to project from, I think his 2010-2012 minor league stats are plus stats for such a young guy, not the negative stats you are making them out to be. Had he started his career in rookie ball, he certainly would have had gaudier minor league stats, but the Giants challenged him at every level.