The protocol is proprietary - and in that case it is in Skype's best interest to maintain a similar look and feel throughout all platforms they support.
This of course doesn't mean that they shouldn't be doing so much more on both systems - I just think in this case the requirement of having a similar application on both systems is necessary.
There's an appropriate saying about history: it doesn't repeat, but it often rhymes.
A good cross-platform app isn't just dumbly copied at the whiteboard stage of MVC planning. It needs to have certain similarities, sure, but the key interface elements will integrate with the host operating system.
Since Windows has window-attached menu bars, why don't cross-platform apps on a Mac have the same thing? Don't say because there's a menubar object to attach commands to. I've seen plenty of apps that use nspopupbuttons to create window-attached menus while clearing the global menu. The reason it's not done is that it's egregiously bad taste. Defeating the user's expectation of how the app interacts with the operating system forces the user to break out of typical interaction into some unknown set by the developer. It's almost never a pleasant transition because someone with the ego to say "do it my way or else" generally doesn't care about testing on users.
In this case, Skype's mistake was breaking OS X's window management portion (Expose), along with the fact that mac applications are almost always one window : one task.
I agree that the application shouldn't be a verbatim copy on each system. There are obviously platform specific UI and methods that need to be adhered to. My point is that the general interface should be similar enough to be able to move a user from one platform to another and they would be comfortable enough to use the application with just the minimal knowledge of that host platform.
I'm not sure the second half of your first sentence follows from the first, but that's not all that important. OP said he'd rather use Mac-only apps, to which the response was "I guess you only want to talk to Mac users." You can very easily have (and there plenty of examples of) Mac-only apps that talk a protocol that also has Win/Linux/Android/iPhone/etc-only apps. You don't have to give up OS-specific design to have interoperability.
My second point was more that Skype should improve the application for both platforms.
Certainly interoperability isn't an issue - the point is that it's in their best interest to maintain a common application interface. For example, I work at a company of 50 people and we have all variations of Mac, Windows and Linux machines running. By being able to support one interface internally it makes it a lot easier - as well as when certain users switch from their Windows machines in the office to their Mac's when working from home.
By way of agreeing with you I will say that yes, easier for IT is "better" than easier for the users, and this has nothing to do with PCs and Macs, it has to do with the fact that there is no spot in the company's financials for the time and efficiency lost by products that do what they are supposed to do, but do it poorly.
Whereas, it's easy to measure the amount of time IT spends supporting the product. So if there are two different UIs, it's easy to see that you need two different training sessions for users, but hard to measure how much time the Mac users lose struggling with the UI.
As I said, this is hardly a Mac/PC thing. You often see it in horribly designed internal applications. It's easy to measure the cost of development but hard to measure the productivity lost due to craptacular UX. So in 2011 I still see RFQs from clients asking for search pages where you fill in a complex form indicating which field you want searched and how to search it, instead of implementing a single full-text search across the application.
You are missing my point, and that could very well by my fault in not explaining it properly.
Why should an end user, who could use multiple platforms, need to understand two different layouts for the same program. This has nothing to do with different vendors, but the fact that a company needs to invest serious time in to developing a UI that is intuitive in all platforms they are targeting. The user experience should be well thought out so that it is a great application that takes advantage of the operating system interfaces that they are working with. If that user experience is lacking then someone dropped the ball - which is a burden for end users, IT folks and so forth.
This of course doesn't mean that they shouldn't be doing so much more on both systems - I just think in this case the requirement of having a similar application on both systems is necessary.