Alright, not sure if this has been discussed yet, but, I'll just add something I'm sure will make things easier.
When you get a message from someone, to reply, you normally have to open the chat window, and find him name on a looooong list, which takes time, and, probably, by that time, your group is chatting with you, then suddenly, someone else messages you, and, you have to keep up with system chat.
So, what I propose, is something like this:
When you get a message from someone, to reply to him, just click his name on your screen when he sends you a message, and it automatically sets him as your recipient for your next messages. Should only work as PMs though.
The chat system could be hardcoded into the game engine and not be able to be changed easily, and with the release of 4.85, the modders and such already have enough on their plates
But yes, good idea. perhaps Shift+clicking, so that you dont accidently pick people up
The command /reply, or /r can be added via FLHook. What it does is send the message to the last person that PMed you. No need for complicated clicky clacky stuff.:P
There are far more possibilities what you can do with FLHook regarding commands.
I just had a swift look at the Hamburg City Server and there is for example the /re command to answer directly without searching for the oter player's name in the list.
They have also kinda dynamic trade routes and a nice escort system there.
So to answer your question: This problem has already been solved but is not implemented in the Discovery mod.