This is part two of my comprehensive look at Manu's struggles. For part one, click here.
The defensive struggles are easy to explain

I won't write 1500 words about it because a) Fred Silva already did that, and b) it's not necessary. Manu Ginobili has not been a particularly good defensive player for a while, but he holds his own and doesn't really hurt the team on that end. Individual defensive rating is not a good measure of defensive competence but Manu fares well on that metric even though he doesn't get the benefit of sharing the court with Leonard and Duncan as often as, say, Danny Green does. His steals per 36 minutes are higher than they have been in years and his defensive rebounding numbers are very good for his position.

So why has Ginobili looked so bad on defense, especially recently? The Spurs have played against teams that like to run two point guard lineups, which has led to Ginobili having to defend guys that are faster than him like Damian Lillard, Maynor, Jarret Jack, Ricky Rubio, etc. At this point in his career Ginobli simply can't guard those guys. They can drive past him on isolations or use ball screens to attack him. Other teams know it and try to take advantage.