The biggest issue is that Signal is really designed to be tied to your smartphone and managed from there. I, and I suspect a lot of other folks who use the desktop app, would prefer Signal to be more platform and device agnostic, like email.

There are ways with the signal-cli utility to make your desktop Signal application the primary signal client, but then managing contacts and groups becomes a real hassle - you have to message with a bunch of json config files and the cli utility doesn't always work as expected.

I'll freely admit, this is probably not an issue for most regular users, but it's still something that could be improved.