This is a lot of hand-wringing over a tiny white number in a red circle. Nonetheless, here are two workarounds for those who dislike it.
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Remove the System Preferences icon from your Dock. There’s no reason it has to be there and System Preferences is always available from the Apple menu or via Spotlight (which can open individual preference panes directly).
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Replace the System Preferences icon with an alias. I don’t know for certain that the alias won’t be badged, but I don’t think it will. I base this on the fact the App Store icon on my Dock is badged, but an alias to it is not (see below). Yes, that alias will have a little alias arrow in the lower-left corner. If that’s too upsetting to your eyes, I can imagine any number of alternative approaches that involve scripting or macros or whatnot that will let you have the picture-perfect icon on something that will launch System Preferences. (Get Info on an app like System Preferences, click the icon, press Command-C to copy, switch to the Info window for your workflow/macro/script/whatever, click the icon in that Info window, and then press Command-V to paste.)
To make the alias, navigate to
/System/Applications/
and start dragging the System Preferences item. Before dropping it, press and hold the Control key to make an alias when you drop it. Drag it to your Dock where you want it (and drag the old one off) and then move the alias somewhere that makes sense to you; perhaps/Applications/Utilities
.