Thing is, for a serial TTL connector to become ubiquitous, it needs to cover at least something like 99% of scenarios. Or maybe 95%. 3.5mm TRS ain't that, and thus just increases general diversity in connectors.
In my experience noise on hot-plugging the serial adapter is a complete nonissue. I'm sure it matters for you, sometimes. But for this kind of embedded work, I'd say it's important far, far less than 1% of the time.
In my experience noise on hot-plugging the serial adapter is a complete nonissue. I'm sure it matters for you, sometimes. But for this kind of embedded work, I'd say it's important far, far less than 1% of the time.