Having published more than 40 apps in the App Store, on behalf of my clients, I'm in a good position to comment on possible ways to improve it.
Perhaps the most glaring omission is the inability to quickly revert to a previous version of an app, once a newer update has been approved and went live. Sometimes mistakes occur, and those mistakes could easily go live. Based on my experience, once an account has a fair number of apps published (like over 30), and an unblemished history, with few app rejections, it seems that Apple's review process gets noticeable lax (as a better word for sloppy). In one instance an app update was glaringly broken on retina display devices (i.e. iPhone 4), yet it was approved and went live.
In such instances your only recourse is to either pull the app from the store, and/or to prepare and issue a new update, but that has to go back to the waiting queue. This could have terrible business consequences, because there wouldn't be a working app available for about a week. You could try to speed it up, by requesting an expedite review. Although the onus is on the developer to test each update before publishing it, it'd be very helpful to be able to revert to a previous, functioning, version.
A related idea would be to have some sort of a staging area, whereby a new app, or an update of an existent app, could be made available through an obscure URL to a set of testers, after it has been reviewed, but before being made available to the public at large. This may be already supported through the option of manually releasing the app after the review completes, though the fact that there's a single URL that points to the app in the store, irrespective of its version, may suggest that the URL points to the latest live version. This staging area mechanism would be similar to the Ad-Hoc distribution, only more scalable.
Another thing missing is an API to access the App Store functionality programatically. Some apps lend themselves to a cookie cutting model, whereby the same template is used to produce multiple apps, perhaps being differentiated by the content they package and some branding. In such instances the ability to programatically interact with the store would be very useful.