I would love the ability to override a usergroup's permissions on a per-forum basis the way you can with vBulletin.
Example: You run a company board, with a "help desk" forum, you want to give members the ability to open/close their own topics in that section, but not across the entire board. At present this cannot be done with IPB3, but it can with vBulletin.
I would also love a "changelog", such that when a member or moderator edits their post after so many minutes the edited-by link would bring up a post comparison option. This would be very useful, if a moderator edits a members post, as you could see what was edited out and compare the versions. It is also useful if a member tries to delete their posts by editing them as you could see what was previously written.
I would like to see the reputation system expanded to include the 'standard' features present in other systems, including the mods for IPB 2.3 and vBulletin:
When giving a member rep, member should be required to enter a reason.
Members should be able to list in their profile, the different reps given to them by other members.
Require members to rep X number of other members, before being allowed to rep the same member again (useful to prevent someone neg-repping the same person over and over).