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It's easiest to load everything using babel-polyfill . I'm not sure what your deployment environment looks, but typically the transpiled code will be bundled up with something like webpack or jspm. A good bundler will minify and optimize the transpiled Javascript code, so you don't really need to worry about "excess" stuff. Detecting native browser support for various ES2015 features is possible, but not really worth it when transpilation + bundling solves this problem in a different way. Detecting and supporting native APIs would add complexity to your application (and thus cost/effort). Of course, if you know you're only using certain ES2015 features, you can manually configure Babel to include just those polyfills. But you will most likely still bundle the code for production.
You should learn them both. Each technology is a tool. Every tool does a job and some tools do some jobs better than others. Django is a very productive framework. It's a complete platform out-of-the-box and has an abundant ecosystem of libraries and frameworks that run on top of it (CMS, ecomm, REST, etc.). Flask is a small core of a framework: the nuts-and-bolts of web development. It's less prescriptive than Django, which means you bring your own set of complimentary tools (persistence/ORMs, template languages, etc.). Learning both and evaluating them in the context of your personal development approach, projects, and teams will let you make an informed decision about when to employ one or the other.