I've developed a rather sophisticated system that may not work for everyone, call it CONTROL-FREAK MESSAGING. Basically, it uses low priority messages for state of realm, vassals, etc., and high priority messages for characters of special interest. Pop-up messages are usually reserved for the really important stuff that pause the game. Everything else goes to the log file.
It takes a little effort to set-up, but essentially the system keeps tabs on people while at the same time not missing a beat within the realm. During war one will be reminded when some other ruler joins the fight, etc., but low priority stuff may easily be ignored.
While this system sounds like a lot of extra work, it's not. When messages pile-up (10 or so), I simply use the list button to check-out what's been happening and check-out individual message(s) by selecting them. When done, I use the Ctrl+<cancel> button (where <cancel> is the red button on the screen) to delete the entire list of messages. In peacetime log files are used to get the news of the world, and s/b hidden during wartime.
HOW TO SET-UP CONTROL-FREAK MESSAGING:
1) Go to messages and set them to default.
2) (left column) Select ruler messages, and go down the list changing every high priority setting to low priority (so it no longer has high priority messages.).
3) (middle column) For one star messages (characters of special interest), change every low priority message to high priority (so it no longer has low priority messages.)
4) (right column) For the two stars messages (all else) change both high and low priority messages to log file only.
SPECIAL NOTE: For sieges and battles; make them all pop-up and all pause the game (cause that's how it works).
REFINE CONTROL-FREAK MESSAGING: With initial settings (above), start a random game and when an unwanted message appears, or appears too often, simply right click it and send it to the log file. After a short while the number of messages will become manageable and very useful. Same thing with pop-ups, if they start becoming annoying just send them to the log file. The log file becomes something of a catch-all that gives one last opportunity to use a message. Then, if the log file becomes less than useful, spammed, etc, then right-click the message and turn it off for good.
-Val