The hardware keys are superior, in many ways, except for customization of course.
However, I have a GNex and I really, REALLY miss them. I wish I had a hardware keys option for GNex because I miss them a lot.
Let me point out why. It's simple, picture this, you pick up your phone and you want to make a phone call, that's why we have it right? Well, you are with the phone in the normal position, assuming you're right handed like me, you're going to pick it up with your right-hand, well, you do this, and immediately hold your PHONE in the normal way, not landscaped of course, but you are on Galaxy Nexus, and you need to CHANGE your hand to CLICK on the power button to show your LOCKSCREEN and be able unlock it to select Phone and dial... If it was a Galaxy SIII for example, all you had to do, was press hardware HOME button (which is in the middle of the phone and accessible both to your right hand and left hand easily) unlock the screen and dial (or even better, unlock the screen isn't even needed if you have the Phone app on Dock which are copied to your Lockscreen)...
So, tell me, WHY is the softkeys so good? Customization? How about usability, when the Home button on phones also works as a Wake up for lockscreen? If I were capable of leaving the Home softkey button at a opacity of 20% or less always on in my GNex even with screen locked I would really appreciate it, but in pocket it may bang and click accidentaly on it and wake the screen unwanted. Also, there's another thing to mention, less screen space, and of course accidentaly press on softkeys, that, above all things are the most annoying, and they happen, believe me.