Can I have a folder (on the home screen) with more than the default amount allowed per folder on the Nexus 5, which is 16? I'm searching a way to make all my games into a single folder. Is there a tweak/app/root command to makes my folders (not storage folders, folders in which you can add shortcuts for apps n' stuff) have, for exemple, multiple pages, kinda like in the IOS system, or a scroll-able folder? Or a way of having a folder in a folder (which would be overkill but hey, it's still a way to enhance the capacity of the folders.)?

I'm using a Nexus 5 running the stock ROM with Android 5.1.1. And I would prefer staying like that, not using Launchers or custom ROMs.

Thanks! ^.^
While there are root apps/extensions such as Xposed GEL Settings that will let you modify all sorts of settings in the Google Now Launcher (formerly Google Experience Launcher), folder capacity limits is not one of them. Google's aware that this bothers people and it's a confirmed change in Android M. As the Google Now Launcher is installed and updated via the Play Store, it's not impossible that we may see this update reach Lollipop as well, but if so, we have no way of knowing when.

Your only option, which I know you're not interested in, is a third-party launcher.