Well, I think you need to ask yourself what you want from the phone. Head to head, the phones have similar capabilities. The Nexus Prime will have a larger screen and Ice Cream Sandwich, but the iPhone 4S will be getting iOS5.
I currently have an EVO 4G that is eligible for an upgrade and am leaning towards the iPhone 4S, because I use the phone primarily for work and need something dependable and solid. The EVO has been good, but not great. Some things are a little glitchy, IMO partly because of Android fragmentation. I feel like the iPhone will be more reliable. I'm also on Sprint, who is rumored to NOT be getting the Prime. If they were, I would have to take a closer look at head to head comparisons once the details of the Prime and Ice Cream Sandwich are available.
Some will point out the anticipated 4G capabilities of the Prime, whereas the iPhone won't utilize LTE or WIMAX. I have to say, I rarely use 4G on my EVO. 4G doesn't make my phone calls any better and drains the battery quickly. If I was doing a lot of web browsing or streaming videos, I'm sure I'd use that feature more.
I don't think you can go wrong with either phone. Part of me feels like the iPhone is getting a bad rap because there are no exterior changes to the device. I read someone say that if the iPhone 4S doesn't look any different from the iPhone 4, then how will people know you are carrying around the latest and greatest device? I say, who cares? I don't view my cell phone as a status symbol, I view it as a device that helps me accomplish things.