An alternative, and with the added flexibility of the use of styles is to create Subscript and Superscript character styles and you can assign them to the built-in styles keyboard shortcuts, or still use a system override[1].
I really dislike the Apple text system sub/superscripts and one advantage of using styled sub/superscript is that compile can convert from the Apple system to (in my case) Pandoc easily; however even then I try to use unicode replacements wherever possible, so for example 1.45×10⁻¹⁷⁸ or CO₂ works wherever unicode does without breaking the text baseline.
[1] and if you really like to customise keyboard shortcuts, you should consider trying BetterTouchTool, works great with Scrivener: boastr.net/