I haven't tried using Message Alerts but by looking at the listed product features, they are focusing on filtering of your email messages and bringing attention to specific emails.
My program works differently as it alerts you when you miss a phone call or sms or email, whatever you choose. It doesn't filter messages but alerts you if you recieve one and don't check your BlackBerry for the specified email. The BlackBerry won't continuously remind you like my program will.
So I think the Message Alerts is ideal for you if you are getting too much email or text messages and want to filter out messages while my program is more for people that are conerned about missing a phone call, voicemail or sms.
Just my impressions by looking at their features though... I would suggest trying them both out as both have trial versions available.