I don't know how easy it would be to implement, but I'd like to see an image duplicate search at the point the file is uploaded, and the file not being permanently saved on the Foundation servers if a duplicate already exists.
I'd also like to see a batch upload interface, something Flickr-ish which permits five or ten images to be uploaded in one action, using the same description and licence tags, something a bit like the Commonplace utility but a web based client, rather than one you need to download.
I know there's a great deal of hatred for the Flickr style interface amongst some Commons users, but I really wouldn't mind the new upload form being the start of something to knock Commons into a more user friendly media repository, I know there's a lot of good work that's gone on already with things like the new search and the suggestive search functions, but I'd like to see more and more features, things like an automatic image syntax generator on each page, so all a user needs to do is copy and paste the code from the image page on Commons into the article on their local Wiki to transclude an image.