I would love to see IP.C support sub-domains. I don't mean installing IP.C on a sub-domain, but kinda like what we have with folders at the moment. So say, domain.com/folder1/ could be folder1.domain.com etc.
Another thing is skin support, if you have multiple skins and you want a certain folder/page to have a different look from the rest, this'd be helpful.
Personally, the threaded view confuses the hell out of me. I can't use a forum which doesn't use the "flat" look by default. Like all software, IP.Board has to get with the times, which is exactly what they've done by cutting out old extinct features. Saves extra code having to be run and makes your site load faster. I think IPS were right to remove these features. What's the point of keeping them there for an amount of users you can count on one hand?