You could probably build a pretty nice (basic) comment system using Channels and Entries if you’re worried about this.
Channel for entries with a relationship to a particular entry. Then have a snippet such as this:-
{reverse_related_entries channel="ch_comment" status="open" sort="desc" orderby="entry_date"}
<h3>{author} said…</h3>
<p> {fi_comment_body}<br />
{/reverse_related_entries}</p>
<p>{!-- Put SAEF Comment form here --}
Using this method you could use statuses for moderation, use SAEF for comment entry (and putting a nice CAPTCHA there), comment pagination, limits and all sorts.
The idea falls apart a little bit when you start with threads, but then perhaps a second relationship of “Parent Comment” could kick in.
Would also allow for nice things such as adding it to a ranking module and allowing users to vote up and down comments in a Digg-like manner, adding “Random Comment” on sidebars and so on.
I’m sure it would need a fair bit of optimisation, but would probably quickly become nicer than the ‘core’ comment module and more future-proof as it follows the EE way of doing things quite strictly.
Food for thought?