ICS is the operating system (OS). Just like Gingerbread and Froyo. Just like Windows 95 or Vista.
HTC skins the OS with Sense, Samsung skins it with Touchwiz. Motorola skins it with Motoblur. The skin changes the look of the user interface (UI), including the font, the icons and the way the phone dialer itself looks. These skins are deeply embedded in the OS and infiltrate so many aspects of it in order to provide even better functionality. At least that is what each manufacturer says. Because of that, it also affects some of the more basic aspects of the operating system. Every phone manufacturer skins the device with their own special something. Not all of them are great. Some are, but it's really a matter of personal preference. I love HTC Sense, my wife prefers Samsung's Touchwiz. And you can always go without any manufacturers changes if you run pure Android, either by installing the correct ROM to your rooted device, or by purchasing the Nexus line of phones that, theoretically, are pure, vanilla Android.
The annoying menu bar is based on the application you're in. If it's optimized for ICS, there is no bar on the bottom of the screen. If it's not an app optimized for ICS you get the menu bar because the app may require it. Remember that devices not built for ICS have 4 keys along the bottom, not three. That missing 4th key is the menu button. ICS doesn't require it so manufacturers got rid of it. As time goes by and more apps are updated to be ICS-friendly, you will see that menu bar less and less.