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You hit the nail on the head why these things are bad. You can either build something on a mass production line, where you're just screwing the same bolt in day in and day out, or become a master craftsman and build it with proper care, design, and quality. These frameworks are nothing more than a factory floor and if all you do is build apps with a framework you're little more than a paid glue stick piecing bits of…
Of course it really is frameworks all the way down. Unless maybe you're building systems by laying out your own transitors. The trick is to understand the strengths and weaknesses of any given framework and match those with the constraints of your project.
Things like jQuery and Underscore on down to stdio.h are libraries. You can pick and choose from what they contain but they're not so tightly coupled that they get in your way.
They're a tool belt with tools that do one thing and do it really well. Frameworks are like having a tool belt with a hammer that also has a saw on the end but in order to use the saw you have to grab the screwdriver even if you're not actually using it.