Short answer: JS, React, Pure, Packages?, Flow Router
Coffeescript / js ?
This one is easy: just use the language you already know.
If you have more experience with Coffeescript than with JS, then why not use Coffeescript?
Otherwise, just use JS.
Also, note than by default, your meteor project supports ES2015, with Babel.
Personally, I use JS.
Blaze/React/Angular?
First, you should read this: Next steps on Blaze and the view layer
Then, personally, I would recommend React.
Having the JS code and HTML in 1 file is convenient, and JS is a more powerful language than any template engine.
You can also have a look at http://riotjs.com, but then you have no official support from the meteor team.
Bootstrap / .. ?
I have no opinion about this one, I never used Bootstrap.
But again, just use the one you already know.
I use http://purecss.io
Folder structure?
This is the most tricky one, especially if your project is big and complex.
I heard that making Packages can help.
Have a look at the source code of Telescope: GitHub - telescopejs/telescope: 🔭 The service ( from Client or Server ) works for render view ( markdown / code / image... ) from fetching URL. · GitHub
Iron/Flow router?
Any router you want, as long as it is NOT reactive (so Flow router, NOT Iron Router)
A reactive router looks convenient at the beginning, but then you keep refreshing the complete page for any little change in your data.
Read this: https://kadira.io/academy/meteor-routing-guide
Good luck 