somewhat related to issue #2132
the default gem file for a new rails app (even called with -J -S) still has the following block in the gem file
group :assets do
gem 'sass-rails', "~> 3.1.0.rc"
gem 'coffee-rails', "~> 3.1.0.rc"
Those are gems not required by the rails gem packages. An user who wishes to use the system installed gems (and only those) would now get additional gems pulled in. This gets especially annoying with the default to run bundler after creating a new app. A bundler run at that stage should be a noop. but with the current settings it isnt.
personally i would prefer the first solution and a default to skip bundler.
The gems in the Gemfile does not need to necessarily be in the rails gem. For example, sqlite3 was never a rails gem dependency but always there in the Gemfile.