Hm, this sounds like wanting to have your cake and eating it, but maybe not.
If you can describe to yourself exactly what you want when, then maybe
you can write the appropriate :setlocal statement for the appropriate
indent options in ~/vimfiles/after/indent/javascript.vim (for Windows)
or in ~/.vim/after/indent/javascript.vim (for Unix-like systems
including Linux and Mac OSX), overriding what is set by defaut when
you have :filetype plugin indent on. The defaut settings are set in
the script $VIMRUNTIME/indent/javascript.vim, which you should not
modify because any change you make in that script can be silently
unmade by any later update of Vim. But you can override all or part of
it by means of an "after" script in your own user space, as described
above.
Best regards,
Tony.