You gain the ability for a user to post more specialized information or stuff they themselves generated without spamming, you get an easy mechanism for another user to post a quick message or even start a discussion with that user, you get the ability for multiple people to join in and make intelligent comments and still have the place readable and organized, and I assume you'd be able to reuse a bunch of code.
Differences from the general board- I'm thinking maybe topics shouldn't get pushed off the bottom? Hopefully that's not a storage issue. Karma could stay the same as normal or you could make it work the same within the topics but not reflect on the users' real score, or you could let just the user who owns that board to give out karma, get rid of it altogether for the user board, or whatever.
[upd. Oh, and also, if things get interesting or there gets to be some important content you could submit a link to that discussion in the general board]
a) Notification when someone replies directly to one's comment.
b) Some way to easily find new comments on a thread. Instead of marking comments read, let me click a page-level button to "reset new marks". Couple that with sorting the front-page by 'number of recent comments'. Especially in periods when the front-page changes infrequently it'll allow users to follow discussions after they've read the submission.
Let me find interesting users and filter them for potential co-founders.
c) Show me users whose submissions and comments I upmod most and who I talk to the most.
d) Provide tags for me to add on my profile: location, horizon to startup, areas of interest, etc. Allow others to set constraints and highlight for them users who match those constraints/tags.
Now that I think about it, another benefit of this is that more relevant news may be surfaced to me - if person X and person Y have a largely overlapping set of upmodded links, then perhaps the set (X-Y) may also be interesting to person Y, and vice versa. Perhaps this could be a way to deal with the perceived quality of news degrading as a site gets more popular as well, as it would allow the system to break off into smaller clusters of news items/people, where each item may be highly relevant to those who belong to the cluster.
Sorry to ramble on like that - I don't expect (or necessarily want) such a complicated feature to be a part of the obviously minimal YC news site...just thought I'd bring it up for discussion.
Edit: Used in combination with jwrecker's idea of having a more personal space, this could be a great startup idea - instead of YC News determining your set of links, it could simply be the set of links you post to your personal space :D
It would be very beneficial to attach faces to the personalities, especially in light of the upcoming Startup School.