Visual Studio Code is a strong candidate. It comes with more stuff out-of-the-box than Atom, and is noticeably faster (despite being built on the same foundation).
It's free and open-source. It's available for Linux and Windows (and Mac). I honestly don't know if it uses GTK on Linux, but it's highly themable, with many third-party themes available.
It comes with syntax highlighting for HTML (not sure about Jinja2), CSS, SCSS, JavaScript, TypeScript (would be weird not to, as it's the primary development language for the whole project), Python, Rust, and C++. (And a ton of others.) Stylus and Vue support is available through extensions.
Has linting for numerous languages, often implemented as integration with established, existing linter projects. I'm confident if you include available extensions, you'll have what you need.
Not sure exactly what features are implied by "code intelligence" but there is definitely IntelliSense support for plenty of languages.
Has Emmet and built-in terminal.
Has Git integration and obviously a plugin system.
Most if not all the other requested features are either also already included or very easily available through extensions.
It's also being improved at a fairly impressive pace. It's a younger project than Atom but has already basically caught up if not exceeded Atom.
Small tidbit for Sublime Text users: VS Code specifically tries to emulate ST's bracket completion behavior rather than Atom's (they are slightly different). There are probably a number of other design decisions where VS Code has tried to follow ST's lead. Though honestly, all three of these editors (Sublime Text, Atom, VS Code) are quite good, and the Internet is full of blog posts and forum comments from people who have switched in all directions (and often back again) among the three.