I should point out that clock speed actually isn't something you can directly compare across different CPU's. 3.2GHz AMD CPU's don't perform the same as 3.2GHz Intel CPU's. It's interesting to see that chart above showing the comparison against the GS2.
If that's the case then I wouldn't be surprised if the Nexus Prime does outperform in this respect.. Although what I've noticed with Apple fans is that when they're outperformed by guts 'it's not about the internals, it's about the whole ecosystem,' but when it does outperform 'well, these other things are so crap because they can't perform along side.' Will be interesting to see the comparisons.
One more thing. What's up with people going on about android having malware??
The Nexus Prime will most likely have a faster CPU in processing power. 1.2Ghz vs 800Mhz. Both will be using Cortex-A9 cores. Not sure about the cache size of each. If the cache sizes are the same, then the Prime will be roughly 50% faster.
The Nexus Prime will most likely have a slower graphics performance. SGX540 versus SGX543MP2. According to the last rumors I saw, the iPhone4S will be 4x the graphics processing power of the Prime.
As for malware, you might want to do some searching yourself for more info, but the general problem is that malware has appeared on various Android application sources including Google's Android Market. At first glance, it doesn't sound that bad because Google can remotely uninstall APK (application packages, like Apple's IPA files).
However, if you dig deeper, it's a little more unsettling.
Because sandboxing on Android is looser, APKs can root the device. If you install an APK that roots the device (whether you explicitly decided to, or it's hidden malware), rooting the device means the APK can edit the device. Removing the APK no longer guarantees undoing the effects of that app, so the recall can and most likely is a broken mechanism.
Common problems for the user have been the fact that some malware authors download other well known apps, install malware in them, and then advertise these in other stores. Since the common user knows of the app by name, if they download one from the wrong source, they could get hit with the malware.
Recently discoveries in HTC's recent firmwares have also shown that diagnostic logging mechanisms installed by HTC (intent was good: to help HTC figure out what went wrong, and help troubleshoot) break the security model further. Basically, any application granted access to the internet (in other words, practically all apps) may request from the diagnostic system almost any piece of data on the entire phone. (not so good.) Without rooting.
In the past, malware was only a problem using Android app sources from random foreign companies. In the past year, as malware writers have advanced, it's a scary world. For my Nexus S, I pretty much download only apps actually issued onto the Android Market from Google or a company I know of well, or use Amazon's app store. For the most part, most apps I download are for my iPad.