David,
Indeed the Cocoon will be too thick for any active use (I own one). I find that if I put my windshirt or rain jacket on instead of a mid-layer, it warms me up just the same as a mid-layer. I would say lighten your jacket to make room for the windshirt, or buy an eVent jacket. I find I can regulate my temperature a little better with a windshirt or eVent jacket than I can with a mid-layer, unzipping the front zip when it gets a little warmer or donning the hood as it gets cooler. Next I would experiment with gloves and hat. You'd be surprised how warm this will keep you while moving!
One of the things I really like about the MTS is that, even though it's a very breathable mesh-like weave (perfect for a summer breeze), it's still relatively thick for a regular shirt. So once you've added a windshirt or jacket to stop the wind, that thickness acts to better insulate you, more so than, for example, a Rail Riders shirt would. Of course a lightweight mid-layer fleece feels more comfortable and relaxed than a windshirt or jacket, so when car camping or around town I will use a fleece mid-layer. But on the trail, I get dual use out of my rain gear which lightens my load, and I find the performance better.
It took me a while to realize that what is really needed when hiking is a wind break, not more insulation. Most of the time what is cooling me off too much when active is any kind of a breeze. For example, I used to wear fleece pants for walks around my house in winter. But the wind would still bite right through and chill me, since fleece is so porous. Ever since switching to wearing my rain pants, I can hike in the same temps with my summer hiking shorts/pants and rain pants, and nothing more. The rain suit blocks the wind from blowing away the heat my body has generated.
Of course, once you've stopped, that's a completely different story; you need insulation to trap body heat, since you are no longer generating enough on your own. That's when I pull out my Cocoon gear.
If I am going to be hiking in sustained, cold rain that's when I will add a mid-layer. The main reason is that the rain will pull heat much faster from the rain jacket than cold dry air, which begins to chill my chest and shoulders too quickly. I will pack a micro-weight short sleeve merino base layer in that case. This gets the merino layer next to my skin, and covers enough of my shoulders to make the difference. My short sleeve merino is 5 or 6 ounces. This also gives me the choice of changing into a dry shirt at camp if I choose not to wear it.