Although it could probably be argued now that Atom has a better plugin ecosystem in regards to your comments about customization.
I haven't really used VSCode much beyond a quick "check out", but the majority of comments I read are the opposite. That Intellisense "just works" and that tern very much suffers from the "open source documentation" issue...
Can you go into some more details about the pain points or some pro/cons of each?
VS Code's intellisense (which uses typescript for both js and ts files) however requires definition files for any dependencies to be installed separately (which may or may not exist/be up to date), requires you to explicitly exclude stuff like your node_modules folder otherwise it will simply stop working with no error message. This gets worse if you have multiple nested node/npm projects as is common with, for example, electron projects where you have to make sure you explicitly exclude the paths to any node_modules directories under the jsconfig.json root and you'll need separate jsconfig.json files for every project (which might be what you want, but isn't strictly required with tern like it is here). Another issue is that since vscode is clearly geared towards typescript, a variable's type is determined when it's declared and only then so something like "let app;" sets the app variable's type to "any" which it stays for the entire file no matter what object is assigned to it later.
There are some things I like, such as the ability to define JSON schemas and a number of the issues above don't apply when using typescript but when writing regular old javascript it's pretty lacking.
WebStorm is doing pretty well, except that I don't like the customization options ( they are 1/10 compared to Atom / Sublime ).
But kudos for Atom team, because they brought Electron, which is a huge game-changer.
It's better because much of the features many people hope to have is built by the professional team and built-in. You don't have to waste a weekend to check 3 alternatives for every feature you want that may not be as good in the end as they are created by developers whose skill vary greatly.
I got tired of tuning the editor when things work out of the box and even better than properly equipped atom/sublime so I can actually get stuff done.
I hope these discussions include more of other non free apps than free vs free.
Outside of that, i havent had this happen. However, if it is simply annoying in your editor you can put them in .gitignore and either tell vscode to not list anything in the .gitignored list, or explicitly ignore files and folders by default.