I know it's not that tough to just delete the message or ignore it, but I'm lazy -- when I log in to one of my teams, I feel compelled to check the "msgs" message in case something needs to be taken care of. I prefer to only see those things that are important and the best way to do that is to give the coach a bigger measure of control over when certain messages display.
Too often, the message is from an assistant telling me that the SG who's been maxed out since the end of last season doesn't need more practice on PER, BH, FT, etc. I know that already - the guy hit his max long ago. Shut the hell up. I'm not changing his practice minutes.
Or else it's a recruit I was watching who is still taking his SATs after I'm done with recruiting. This matters quite a bit to my D2 team, but not once signings are over. And it doesn't matter at all to my D3 team. I think I can turn those off by "removing" the player from my watch list (though I'm not 100% sure on that). If I want to keep him on the list for next year when he doesn't sign, then I just have to put up with the messages whenever he takes another SAT. It feels like spam.
The ideal solution in my mind would be the ability to turn off messages involving individual players - maybe a check box on their Recruiting panel that turns eligibility messages on/off. It sure would cut down the spam for busy coaches. After all, we get paid the big bucks for things other than babysitting maxed out players or kids who can't get the requisite score on a test.