Besides the obvious (hah).
I'm still no sure why you would choose either of those.
I used to think compiling a single file was easier, as you use <reference>s to link files and can use nested modules to manage a global namespace.
But now I'm thinking that import/require and many output files might be good for greater modularity (and similarity to regular JavaScript / ES6).
But can you namespace types adequately using imports? Using extra level of modules seems awkward when importing.
And won't we still need <references> to resolve the type annotations?
How do I decide on this?