I understand the "command line can be more powerful than the UI" practice, but the UI is not simply leaving out an "advanced" feature, it is actually misleading the admin in a big way.
When I go into IIS and edit properties at the server level, I expect it to affect the server (all sites). When I edit the properties of a single website, I expect it to affect only that website. In the scenario in this thread, editing a property of a single site climbs all the way back up to the global level. This is wrong, and misleading. No reasonable admin would expect or anticipate this.
Everywhere in the IIS 7 UI, there are links in the action pane to "Revert to Parent" (discard the locally configured property, and inherit from above), reinforcing the hierarchical nature of the IIS config structure. And this has been this way in past versions as well, and makes sense. There are configs at the server level all the way down to the site level and even to the file level.
Why would any admin think that changing a single site property would ripple out to every other site on the server?
Also, the UI (as I mentioned earlier) goes out of its way to explicitly grey out the host header field when adding an HTTPS binding. Why would it do that, if host headers are perfectly acceptable, allowed, and even configurable in all other ways? It’s strange that you would actually grey out a config field that is allowed and supported.
As for the UI design issues of things like "ask[ing] you if you wanted us to delete it if it was the last one, etc.", isn't that what it should do? This is done elsewhere in other service UIs and wizards (Active Directory wizards, DFS MMCs, etc.). In DFS, for example, removing the last folder target also prompts to say there are no link targets, and asks if you would like to remove the replication configuration info for the DFS folder. It asks because it NEEDS to ask, because you can have DFS replication without the DFS targets explicitly defined as a DFS share. So, rather than make a significant change like removing file replication, it does what it should - it ASKS if this is what you want, it doesn't assume and cut the admin out of the decision entirely.
Shouldn't this be exactly what happens in IIS? Dependency checking is common, smart, helpful, and a sign of well-written and well-thought-out code. A single prompt or two is a more than acceptable alternative than simply making assumptions and breaking an entire server configuration. The UI is not making things simpler; it just willfully ignores the required complexity.