There are fundamental differences between the iPhone/iPad(iDevices) and the computer beyond the touchscreen/mouse difference. Yes, that makes designing for the three different platforms radically different. But, there are still other contributing factors that affect both the design as well as the overall experience of the different platforms.
The first major difference is the open/closed filing system. My computer has a open filing system in that I have access to all of my files on this computer from the Finder. I can go to a file in the Finder and open it up in whatever program I want that can read it. I can also open up a program that I know can read that file, and load it from inside of the program. I can also see every script, image, and document that goes into running that same program in the Finder. Some Apple programs like iPhoto try to hide my photo files from me by putting them inside of the iPhoto app in my Applications folder. But I can right click the iPhoto app file and choose "Show Package Contents" and it will give me direct access to the files. All of this direct access lets me create the experience that I want pretty easily. And for a computer, that's what I want, something that I have strong control over and use how I choose. I interact with it for longer periods of time and more intensely and I expect it to be able to handle whatever I throw at it. The iDevices have a closed system that doesn't allow me direct access to my files. For example, I have to use the Photos app to access my photo files, and I have no easy way to get direct access to them. It's what makes the iDevices so simple and clutter free, but also much more limiting. This decision pretty much forces me, the user, to experience everything the way the designers intended. That's not to say it's wrong for them to do this, every aspect of the iPhone was created to be easy and fast to use. This is what makes interacting with iDevices so nice. With something that is so much smaller than a computer and intended for on-the-go use, simple makes sense, and it's what I want.
This control over the experience on the iDevices continues into the actual design of everything, as well. Any computer, mac or otherwise, all has a design aesthetic to it. It always has, and always will. But that aesthetic doesn't ever really influence how a website is designed*. A website is completely separate from the computer, design and otherwise. There is somewhat of a visual language across websites in general, how things are layer out and identified. But why does it have to be how people are doing it? Can't it be changed up for the better? Rethought completely? iDevices are the complete opposite of the computer. Apps are programs running on the iDevice itself, and it's treated as such visually. Because the app takes over the entire screen, and that's the only thing the iDevice is running, it's become standard practice to design the app in the style of the iDevice. iDevices have a very specific visual language to them unlike any other OS, and apps tend to take this visual language and tweak it to fit their wants and needs. But this is something that I want to question and possibly change up.
*However, technically, a website doesn't fully correlate to an app on an iDevice, a program running on the computer would (ie, an app from the Mac App Store). But let's stick with website equaling an app, because that's pretty much the standard right now. However, Apple does seem to be attempting to turn the mac computer into the same closed system design of the iDevices.