For a start, I don't think you have a sufficient amount of ram to utilize all the processors, so it's not surprising that the processors aren't the bottleneck. I would check to see if your ram is being completely tapped out during the render, and if so, it would explain why you aren't seeing your CPU being fully utilized.
For reference, I have a Mac Pro with 8 cores, and 128GB of ram, and under many circumstances AE uses all of it.
Thanks for the response, Arivl. I'm sure you're right about the mismatch of RAM and processors, but it still doesn't explain why it isn't outperforming a machine with one quarter the RAM. Shouldn't it be at least twice as fast as the iMac if I allocate 8 cores and 16 GB of RAM, versus the maximum 4 cores and 8 GB available on the iMac?
There's plenty of debate about the new Mac Pro vs a kitted out iMac. Benchmarks show that some iMac After Effects processing can actually be faster than on a Mac Pro, depending on the content and some other factors. If you're using software that has been optimised for the Mac Pro's GPU-centric architecture, like Final Cut Pro X, you will see great benefits.
In my own facility recently we opted out of purchasing Mac Pros this year, and bought top-end iMacs instead. The benefit to cost ratio simply didn't make sense for us right now. Mac Pros are awesome machines, but a significant component of their cost is the dual GPUs, which are simply no benefit to After Effects.
Reports say that the After Effects engineers are working on a major revamp of the After Effects processing system, so I'm betting you will realise far greater benefits from your Mac pro in coming AE versions. For now, you may continue to see performance that is not spectacularly better than a souped-up iMac, depending on the type of processing involved.
I've seen a few benchmarks that suggest the 8 core systems give better bang-for-buck than the 12 cores. Try reducing your processors to 8 in After Effects and see if it makes a difference. With 8 cores, allocate 3GB of RAM per core to leave some RAM for the OS.
Oliver, you're right in principle that more ram should enable you to use more processors, but the truth is that AE often is unable to hand multiprocessing efficiently. As you know, depending on the project, it's sometimes better to have multiprocessing disabled entirely, but even in those situations where it lends some advantage, it might still not be better than having fewer, faster processors.
If you post a link to a collected test project and your render times (both nMP and iMac), I can try rendering it on my system to see where the bottleneck is.