The problem with the \(..\) and \[..\] forms is that \( and \[ already have clear and important meanings in CommonMark (and other Markdown versions). They are escaped parentheses and backslashes. It’s very important to keep this behavior, or you’re left without an easy way to write literal special characters when this is needed.
Hence I prefer the $ syntax. Pandoc has supported this for a decade now, with some simple heuristics that prevent unwanted capture of regular $ characters. This has worked just fine. It’s extremely uncommon to write things like US$50,000, and one can always escape the $ in cases like this. Anyway, my experience with pandoc is that this is not a pain point. People simply don’t complain about unwanted capturing of $ characters.