I'm not sure if this is a good idea or not, and I'm not sure anyone except maybe JP Lang would know the best course of action.

There are already some discussions about this topic

Like: message#31117

And there are already some efforts
https://github.com/Tab10id/redmine_plugin_asset_pipeline

Move existing application.js contents to some other file like base.js and include it via asset pipeline and enable plugins to add their own js to application.js as a manifest which would compile application.js later

So eventually it would look like this

// This is a manifest file that'll be compiled into application.js, which will include all the files
// listed below.
//
// Any JavaScript/Coffee file within this directory, lib/assets/javascripts, vendor/assets/javascripts,
// or any plugin's vendor/assets/javascripts directory can be referenced here using a relative path.
//
// It's not advisable to add code directly here, but if you do, it'll appear at the bottom of the
// compiled file.
//
// Read Sprockets README (https://github.com/rails/sprockets#sprockets-directives) for details
// about supported directives.
//
//= require jquery
//= require base
//= require whatever from plugns...