In re-designing the App Store for the iPad, Apple has done some fairly subtle and some fairly bold changes both of which are negatively affecting consumers and developers.
As a consumer my first observation about the iPad App Store was that it was frustrating to browse. On the iPhone, the App Store is mostly controlled with "flick" gestures. For example, when searching for an app, it's easy to browse twenty-five of them at a time by quickly scrolling up or down and then touching "Twenty Five More..." The iPad offers a vastly different experience. First, the initial search results page has iPad and iPhone apps competing with each other. Secondly and more oddly, even with a much larger screen, only twelve apps at a time are presented. Seeing the second page of twelve apps requires pressing the right arrow. With the iPhone App Store, it is possible to flick down to view the first set of twenty-five apps along with the second set. The iPad paradigm of arrows necessitates that only twelve apps only ever be present on the screen, with considerable effort required to move from page to page.
While there are considerably less iPad apps available right now compared to iPhone apps, the changes to search alone will impact app developers. As with the iPhone App Store, search ranks are dependent on factors such as the number of downloads and the least popular applications will appear outside of the first several sets of results. The iPad presents a more significant disadvantage, however, due its paging metaphor. It will take more time for consumers to see the more lowly ranked apps. It's also very likely that they'll simply never reach them, resulting in the popular apps having a higher likelihood to stay popular.
Apple also approached the "Categories" view differently on the iPad. They introduced the "In the Spotlight" view, where screens from featured apps can be browsed in cover flow. The more traditional category view can be accessed from this area but Apple also overhauled it by removing the explicit breakdown of viewing apps by paid, free, and release date. Instead, Apple decided to mix paid and free apps together, sorting them by default as "Featured" in a drop-down filter (the other options are "Name" and "Release Date").
While it's a more subtle change, this again gives preference to the most popular apps requiring a consumer to change the less obvious sort filter to "Release Date" in order to see the actual new apps. Free apps also have an order of magnitude difference in download totals, so while I'm sure Apple has a means to account for that, it's not exactly clear to me how that will be taken into consideration in the default "Featured" sort. Unless Apple were to add back in the paid versus free distinction (which I would think is likely), this revised category view would likely alter many developer's approach to launching free apps as a means to get visibility for the premium or "pro" versions of their app.
One would think that the iPad App Store represents Apple's most current thinking about how their App Stores should operate (iTunes, iPad, and iPhone). If that's the case, then it is evident that Apple wants to cater more to consumers and the most successful developers. Unless upstarts or independent developers somehow get featured by Apple, it's going to be substantially harder to have their iPad apps be discovered and receive the visibility needed to make developing for this device worthwhile. Of course, it's only fair to realize that the iPad App Store is brand new and will evolve over time.