Preference, of course. Here are some features that may appeal to many users.
It remembers all the sessions that were open and the directory the shell was in when Yet Another Rebooting Update comes through. Obviously the local command history is lost, but even just restoring the tabs, putting back their titles and changing back to the right directory is a monster time saver.
Being open source is a very real benefit in my life, even if I never change a thing, because I can change a thing.
The colored tabs are also pretty.
I believe Terminal does this as well.
Just so you know, it has long (always?, can't remember back to 10.0 and before that clearly anymore) been possible do this for arbitrary application menu commands system wide in OS X with no specific application support whatsoever. In System Preferences, go to Keyboard Shortcuts and then Application Shortcuts. You can then add new entries (either system wide or for a given app), the exact name of the menu command, and then a shortcut, and yes you can use this to change an existing supplied one. I use this in many places including Terminal, but what originally drove me to find this feature was browsing. I'd have a few dozen windows open full of sites I was using for a project, then go to hit command-w to close a window/tab and hit command-q instead, closing everything and forcing a full reload to my immense rage each time. Now Safari, Chromium etc are all Control-Command-Q for "Quit", in the Finder "Print" is Control-Command-P (I basically never want to print from the Finder), etc.
So while having fully arbitrary internal shortcut control is a mild convenience and decent power user bullet point, for simple cases at least it's also just that, a mild convenience. The same can be accomplished anyway. Which in my opinion is how it should be, power users should be able to trivially change shortcuts to whatever and application authors shouldn't need to worry about going to specific work to make that possible, this is the sort of thing that should be handled by the OS.