I'm using oh-my-zsh with the bundler plugin, which aliases all binstubs to a function that prepends bundle exec if there's a Gemfile. It works very well in practice. rbenv handles the correct ruby version, Bundler loads the right gem, and it all falls back to the newest version on the system default ruby.

It's a few more moving parts behind the scenes than I'd prefer, but once configured it's completely transparent.