Take it for what it's worth, because I'm still trying to break through and get picked up somewhere too. But every package I've submitted thus far has included a cover letter/letter of introduction, even if the req's did not specifically call it out.
Just a basic overview of who you are and why you want to do this, your background, where you're at in life re: education/civilian or military employment/any flight experience, etc. You just want the person/people going through your package to get an idea of who you are and what you're about beyond a couple of test scores, transcripts, etc. That's how I look at it anyway.
Honestly I'm not sure if it's better to acknowledge weak points and address them, or just hit the high points and emphasize them...I guess it's a fine line and probably just depends on who's reading it. Someone who's actually sat on the other side of the table could probably speak to this better.