Here's what I've come up with in the time I've been here (count any duplicates as seconding the prior comment). WARNING: Long post ahead!
Full text of comments/shouts on the Updates page in the control panel, with ability to reply directly to it with the click of a link.
deviantART-style AJAX-based inline commenting rather than having to go to a new page.
Links don't move halfway across the screen when you go into your control panel.
Setting number of thumbnails per page is saved as a permanent user setting rather than having to be re-set every time (and while I'm at it, changing the number automatically reformats the page rather than having to click "Apply").
Greatly expanded commission info page, with, among other things, the ability to set one's own categories (if you've ever used the thing on LiveJournal that creates your linkbar, it would work like that only each item would have fields for both the category name and the price). Possibly change the sample link to display a thumbnail instead of the URL.
Separate galleries for stuff you created and stuff others created for you. Possibly coupled with the ability to "tag" other people's submissions as having been done for you, like how Facebook lets you tag other people's photos of you. So the new "Gift art/Commissions" gallery would contain unattributed stuff you submitted, and stuff from other people's regular galleries. Unattributed ones could have a "Claim credit for this" link that auto-sends a confirmation request to the user's /msg/others page.
If there is no Featured Submission set, that panel just plain doesn't display instead of containing an error.
Viewing Mature and Adult art can be toggled separately.
Smaller, less fancy emotes. I hate how the winking one looks like an evil grin.
Working quote tags in PMs. This probably bugs me more than anything else.
"Favorite website" ought to have a title field as well as a URL. As it is, it's confusing to some users (I've seen plenty pages where they entered a title instead of a URL) and, even when it's done right, results in vague, non-descriptive links.
Alert bar: change "S" to "A" (for Art, duh

) and add a new "S" for shouts.
The option to turn off watching someone's journal.
Better system for info previews than the hovering description. I suggested a possible replacement for this
here but it needs fine-tuning.
I'll add more if I think of them, but that's the bulk of it.