I think Notification Centre needs more options. Only ~5% of my email ever shows up there because I have a long set of Mail rules to sort incoming messages into folders. Sorted messages don't appear.
I don't really find it useful for most other apps because I cannot customize the notifications by app, subject, person or anything really. With Growl I could see in my peripheral vision whether a notice was a meeting request, a message from a co-worker or just something from Twitter. Important events were assigned custom sounds so I didn't even need to look to know what they were. In Notification Center everything looks more or less the same and, as noted earlier, most of my email never even shows up.
Another feature that's been driving me crazy is trying to move windows to another desktop. Back in Spaces I could drag a window to the edge of the screen and you'd switch to that space. Now I have to open the Mission Control view, try to locate the miniaturized window I was trying to move, drag it to the new desktop and then switch to that desktop. I also really liked the physical layout of the different spaces. They had a location not just a number.
I'm quite sure the unnecessary skeuomorphism will be gone from things like Calendar and Contacts. Hopefully usability will also be improved and not just the look.
Hopefully iCloud will gain sharing capabilities. The automatic syncing is really great, but there are things I want to have automatically synced with my wife's computer. Having different Apple IDs makes that a cumbersome manual process.
On the same theme I'm hoping Apple figures out collaboration through iCloud or some similar mechanism. A smart combination of Dropbox and GoogleDocs should be possible, but Apple currently shows no signs that they want to address that market.
The sandbox and versioning system that locks documents to a single application needs rethinking too. Having basic text documents that you can't even see from an iPad is ridiculous. iPhoto offers "edit in an external editor" so it's clear that at least one person at Apple knows that files are sometimes opened by other apps.
I'd like to see more options for colour icons and such too. Give us the ability to make things quicker and easier to use.