When comparing JSPM vs Yarn, the Slant community recommends Yarn for most people. In the question“What are the best front-end package managers?” Yarn is ranked 1st while JSPM is ranked 3rd. The most important reason people chose Yarn is:
One of the most important aspects of Yarn is determinism (predictability). The lock file ensures that the same dependencies will always be installed in the same way and order regardless of the machine for a given repository.
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Pros

Pro Registry agnostic
JSPM is registry agnostic, it can pull packages from npm and github and is built in such a way it can support more.

Pro Module style agnostic
Loads ES6, AMD, CommonJS and globals.
Pro Can transcompile ES6, JSX and Typescript
Pro Much faster than Webpack or Browserify
While Webpack and Browserify recompile the source code using Babel, jspm is the only packager that can load prebuild/minified code downloaded from the npm registry.
Pro Bundled based on imported modules without any config
Create the bundle file without config and add only the modules imported.
Pro Switch between async or sync load
With a simple command you could change between load the modules async by systemjs or sync with a bundle file.
Pro Easy install packages from npm, github or any git repository
Pro Versioned package urls
It creates a packages folders which are versioned. This makes it future proof for a time where we stop bundling all the code. In the following presentation Guy Bedford calls bundling an anti-pattern.
Pro Very easy to start with

Pro The same results will be yielded every time yarn is run in a repository
One of the most important aspects of Yarn is determinism (predictability). The lock file ensures that the same dependencies will always be installed in the same way and order regardless of the machine for a given repository.
Pro Can tell you why a package was installed
yarn why <query>
can tell you why a package was installed and what other packages depend on it.

Pro Good network performance
Yarn efficiently queues up requests and avoids request waterfalls in order to maximize network utilization.

Pro Offline mode
If you've installed a package before, you can install it again without any internet connection.

Pro Flat Mode
Resolve mismatching versions of dependencies to a single version to avoid creating duplicates.

Pro Multiple registries
Install any package from either npm or Bower and keep your package workflow the same.

Pro Network resilience
A single request failing won't cause an install to fail. Requests are retried upon failure.

Pro Good documentation
It looks like it has good documentation.
Pro Security is put at the forefront
Even though it's still in its early stages of development, security is one of the core values on which Yarn is built. It uses checksums to verify the integrity of every package before executing its code. This also helps avoiding errors related to faulty caching or captive portals.
Further steps are also being taken to improve the security of Yarn which will be implemented in the future.
Pro Built by the community for the community
Even though it's backed by Facebook, Yarn is built as a community project first and foremost. It's completely open source and hosted on Github. It's released under a standard open source client and has its own GitHub organization and set up to work under the same governance model that other successful projects have used in the past, such as Rust and Ember.
All of this means that both existing and new contributors will always work together to improve the product and introduce new features while also keeping in mind suggestions coming from the community.

Pro Backed by Facebook and Google
Was created in a collaboration of Facebook with Exponent, Google and Tilde.
Cons
Con You need to be an expert to write shims
You can load any module. But that comes with the price:
you need to find or write configs to load a particular rare module.
Con Doesn't hide complexity
JSPM doesn't try to hide complexity from the user. I.e. when some issue emerges you need understand a lot to be able to patch it or create a workaround.
Con Watcher has bugs
Watching would benefit from improvements
Con Unstable API
0.17 is still in beta. 0.16 is lacking features.

Con Poor bundler performance
Bundling performance is slow, though offset by the fact that bundling is not required during development, since it can load dependencies asynchronously.
Con Takes up disk space
Yarn adds to your disk space usage since it stores dependencies locally.
