The Addon Manager doesn't have anything to do with the stuttering. And not the scenery, apart the fact that our sceneries are WAY more detailed (especially textures) that the one you mentioned. Scenery area it's not the only parameter to compare two sceneries, you should obviously compare graphic quality.
For example, sceneries that don't use any of the advanced FSX materials, so they look like a FS2000, use the fastest possible shader and, there's much less load on the bus, because the quantity of data moved is a lot less, without specular+bump mapping, for example. Just compare the texture folders sizes, this is a better indication of the size than just the scenery area.
Since very few developers fully use FSX materials, because they usually start developing in FS9 and then move to FSX, there aren't many sceneries around with those demands. Those that are, are much slower than ours.
However, THANKS to the Addon Manager, that allows several optimizations that FSX BGL-only sceneries can't use anymore (like LOD, selective loading with realtime checks for distance, viewpoint and altituide), our sceneries have similar fps comparing to other sceneries that, of course, looks much worse. If we did an FS2000-like scenery in FSX, with all our Addon Manager optimizations, we might double the fps...
So, it's exactly the opposite. The Addon Manager, as clearly explaiained in the FAQ, DOES NOT handle "just" the protection. That one is simply ONE of its features. But, unfortunately, since is the only one that end users gets in touch with when they buy the product, they mistakenly assume it does only that. That's why we wrote a FAQ for this...
You probably assumed that the Addon Manager have something to do with this, because you thought it is a common element between Cloud9 and FSDT sceneries. But the common element, instead, it's a way more important one: the designer and how the sceneries are done, since even the older FSX sceneries we made for Cloud9, were already fully using FSX methods.
So, the Addon Manager, instead, HELPS with performances. Without the Addon Manager, the scenery would have been much slower. In fact, we might not even started working on a JFK scenery, which many others thought it wasn't even possible in FSX. We know this very well because, in the initial stages of developement, we don't configure the scenery to run under the Addon Manager and, as soon as all the objects are in, we have very bad fps. So, we know that's the time to create the "Addon Manager" version of it, and we immediately gain our desidered fps back.
And, the fact you have seeing this in FS9, clearly proves the Addon Manager doesn't have anything to do with it. Well, of course you might thing it does, because you can see there's an FS9 version of it and, without knowing how it works, you might think this is the case. However, the FS9 version is so vastly different, and based on an entirely different principles, that the only thing in common it has with the FSX version, it's the name.
About micro-stuttering, it's a problem that it's inherent with very high performance systems, and it's related mostly to bus and bandwidth traffic. There are a lot of explanations for this, so I'm not going to repeat them. Have a look at this thread on Avsim:
http://forums1.avsim.net/index.php?showtopic=245251Which discusses a DX frame limiter, which seems to make a very good job optimizing the bandwidth traffic. Please, read all the thread, because it contains very useful information about the issue, which IS more apparent, the faster your system is. I suggest you to try that one.
Also, together with the frame limiter, you might want to play with the BufferPool setting as well, and with the Addon Manager it's possible to set this without even editing the FSX.CFG file.
Also, I see from your video that you are using the FSX fps limiter, which (if you follow the above Avsim thread), it's not something that works very well in very dense areas or big airports. Usually, the best solution would be running with the FSX limiter off in the airports/cities, and with the limiter on in the countryside. However, if you use this new fps limiter, it's best to always turn off the FSX limiter.