I checked the performance reports, and I can't seem to find one with your username or information.
If you could, run the performance test, and send feedback. In the notes section, put something in there that I can use to find the report. Like Atten: C7, or Camacha's performance report. I'll look into what's causing slowdowns for you.
In regards to the cpu usage. It's very rare that you'll see an application use all of your cores to the max, there's a lot of reasons for this, including issues with thread priority on a modern operating system.
If you're interested in the technical details. There's a detailed explanation below. But, in regards to the stuttering, we have a pretty good idea what's causing that and we're working on a solution. We've made some major changes to the physics engine, and rendering systems that should address a lot of this. The current version you're using is an in-between, and this is a case of it getting a bit worse before it gets better.
Technical Info :
Part of the problem is that we're not going to achieve 100% efficiency of threading. We can only use multi-theading in very specific areas, and we try to focus on using it in high frequency code where we can get the most benefit. Unity engine is itself threaded and uses multiple processors for script execution and rendering tasks, but it's not "thread-safe". What that means is, we can't interact with Unity's data or objects inside of a thread that we make, we can only do so when we are allowed to in Unity's sequential script execution.
We get around this a bit by utilizing OpenCL, where we can dispatch a work packet or kernel, to various types of hardware, including a cpu or gpu. This lets us take advantage of lower level optimizations and feature sets that the hardware supports. (Such as sse). However, we currently have to call even the OpenCL job in sequence, which means, we start the work (let it compute on multiple processors), and then we continue after it has completely finished. Ideally we'd be able to just let physics run completely asynchronously in its own threads and "sync" with Unity when we're allowed to. Maybe we'll be able to do that at some point, but right now we're just doing our best to work around the issues at hand, to give the best performance possible.