The issue is for developers. The duopoly means developers who demand a first-class mobile presence are forced to abide by Apple's rules.
Would Spotify exist today if Apple disallowed its presence in the App Store? That's 60%+ of US mobile subscribers only reachable via the "open web"; a poor experience for a mobile music player. Its likely they would not exist; but Apple Music would.
This may sound like a theoretical argument; a problem that isn't a problem because obviously Apple allows Spotify. But consider cloud game streaming services; these compete directly with Apple's mobile gaming revenue. Apple won't allow them on the store. When you get right down to it, their only sin is that, unlike Netflix, Spotify, and Kindle; cloud game streaming apps do not pre-date the App Store. That's the only reason these other cloud media streaming apps are allowed; consumers adopted the iPhone with expectations concerning the nature of their existence. Apple got there first on gaming, then shut the door.
Thus, the greatest sin of the iPhone is its behavior toward destroying true innovation. Not a slightly better note-taker or a prettier weather forecast; the App Store is great at distributing that. But, rather, applications Apple hasn't foreseen, now hampered by both the App Store's distribution rules, financial rules, and more fundamentally, the intentionally limited operating system.
This is not a situation where these innovations can't exist on the iPhone, but will flourish elsewhere; Apple's stranglehold on the consumer US smartphone market, the primary means of computing for many, many people, means these innovations may never exist at all. Possibly because they can't find a market. Or, more disturbingly; because they would have been invented by our next generation's Steve Wozniak or John Carmack, but instead of growing up with a computing environment which (safely!) nurtures creation, they grew up with the iPhone. And maybe an iPad.