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There are a few reasons for this, but a big one is that the way Netflix's presents content can sever the tie between a network and the show. When you watch a show on Netflix, most times it doesn't bear the original network's name. So you have no idea who actually shelled out the money to make "Breaking Bad," or "Gotham," or whatever. This undercuts the value of the show for the network.
HitFix's Alan Sepinwall recently asked Netflix content chief Ted Sarandos about this phenomenon, noting that many Netflix viewers have no association between programs like "Breaking Bad" and AMC, the network that produced it.
"You see that over and over again," Sarandos replied. "I'm sure more people watch 'Portlandia' on Netflix than ever see it on IFC. And that's not the intent. The intent is that it builds their show's brand, which it does help. And they inch up their audience a little bit every time on the network. But for most people that's a Netflix experience, not an IFC or an AMC experience [with 'Breaking Bad']."
Here, Sarandos admits that Netflix's way of distributing shows downplays the role of the network. If Netflix customers don't associate "Breaking Bad" with AMC, this undermines the show's value for the network. Sarandos presents this as an unintended consequence, but Netflix does choose to strip the branding off old shows it licenses. That's not an accident.
Some networks have begun to push back on this, ABC in particular. Here's a screenshot of how ABC's shows retain branding on Netflix compared to those of other networks:
Netflix
Sarandos' main argument is that the positive effect Netflix has on the "show's brand" outweighs the harm of the show becoming a "Netflix experience" for many, instead of an AMC or IFC one. But if ABC is any indication, networks may start to fight to get more credit for their shows, instead of ceding that to Netflix.
The fact that many networks allowed their branding to be taken off might simply be a leftover from the era of cable TV reruns, which usually do not carry the mark of the original network. But Netflix is a different force altogether than cable reruns. And even Sarandos admit that Netflix gets a lot of credit for award-winning TV shows it didn't have a hand in creating, like "Breaking Bad."