So we finally have an in-game chat system, and though it has many many issues, we know how it works and it is wonderful! So now let's talk about an in-game MESSAGING system.

ACCESS LOCATION:
In-Game, have a permanent button next to Global Chat
Website, Account -> Messages

CONSTANT FEATURES:
Inbox, drafts, sent, and important.
Quotes possible inside the messages
*Important would be for things you know you will want to keep, whereas if you're unsure or don't care, just leave it in sent. The Important folder could also have a bunch of extra features, maybe, such as being able to organize the messages in any order (rather than filtering different ways), different displays, etc

EARNED FEATURES:
Be able to change the color of specific messages from other accounts (including the Bot)

BOT:
There needs to be a bot account. It will automatically send tournament updates, contest details, and trade notifications (such as my suggestion in the trade thread "Have a notification when you receive a card in a pack or sealed game, that you are requesting in an open trade")
Messages from the Bot will be in a specific color, even before players gain the ability to change the colors

NECESSITIES:
If it's possible (I'm not 100% sure it is) the in-game messaging system NEEDS to be linked with the online PM's

It needs working scrollbar and custom groups ( not only global chat ). I dont think anything else is important now. I would focus on other things.

scroll bars, deffinately

What do you mean by custom groups?

Yes i know this isn't of huge importance, but it will need to be implemented sooner or later, and it's always good to help get an idea rolling. Less work/stress for the devs when the time comes

chat rooms

Just look at current IM software and do it the same way. or buy the code
The current system kinda serves its purpose but if you look at what could be possible, it's much inferior.

There needs to be both a chat system AND a messaging system. They should not be the same thing.

Also, an extra suggestion: EARNED FEATURE: Allow players to automatically delete automated messages from the bot (so you can avoid Tournament Notifications, for example)