Are you talking about Private Messages? Or maybe bulletin board comments on profiles?
Either way, it's true that they're functionally rather limited. But they're really not intended for deep, complex organization or communication. It's better to use actual WikiTree profiles.
Also, once you've communicated with someone once, or are on the same Trusted List with them, you have their e-mail address and can communicate directly. The Private Message system isn't meant to be a replacement for e-mail. It's just a way to protect your e-mail address while allowing people to get ahold of you.