I've been thinking about this one, and here's why it's good that they are separate:
I don't get these e-mails daily. I get the matched FS list (even as small as that is) more often than the matched your wantlist. They help me realize that stuff hit.
If you find that you are getting them too much, you can turn them off (on your profile) and you can just navigate to those pages when you feel like it to see the matches.
And yes, the message system on here is a little too basic, but, it's a database, not an e-mail platform.
-- Dan --
Note: Please see my profile for more info regarding trading (section updated 3/4/2024). I have added a large portion of my inventory to the site, and currently have trading turned on (details are in my profile).