Fair enough. My primary concern is players missing important messages in different chat rooms.
However, chat commands are still powerful tools for power users. Their function should be available for new users in an easy-to-use format like you want, but they should also be available directly on the chatline to power users like I want.
I definitely like the idea of different colors or other "hints" on where a message comes from, all together in the same chat window. They don't need to be different colors if it's clear where they come from. For example, a message list might look like this:
Whisper: System MOTD Bot: You are on the RandomUniverse Server.
Whisper: System MOTD Bot: Please follow the rules as posted.
Global: System MOTD Bot: Warning! There is an anomaly reported in 256, 256, 256.
Nearby: RandomPlayerName1: Does anyone have an extra rocket launcher?
Nearby: RandomPlayerName2: Yes, but you need to pay me 30 shield caps for it.
Galaxy: RandomPlayerName3: The hawk has landed at 304,407,110. Attack.
Sector: TraderNPC1: Sector 2,2,2 is protected. Hostile action is not tolerated.
(Now that I can actually see it, I really like the different colors from different "chat rooms".)
It would be good for players to be able to easily "subscribe" and "unsubscribe" to different channels. (Players will want to be able to unsubscribe from different channels, at least temporarily, to focus on more important messages and avoid clutter.)
It would also be real neat and useful if you can hover a mouse cursor over a line in chat and get additional information in a temporary pop-up.
Example additional information: Origin sector (could be modified or blanked-out by electronic warfare!), whether it is to you in particular or a broadcast message for all, details on the source, such as their faction, if known, and maybe an "options" button to change chat settings on the fly, like the client's global text color and subscriptions.