Just to help put this in perspective I did a few tests... I don't want to rain on the parade but I feel this may not be practical without changes to AS from the developers side.
I am not shooting down the idea. I just want to let you know what I know about massive layer counts and multiple complex vector layers.
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Layer Count and Performance
I did a quick test and found that after adding about 800 layers or so to an AS document (not in a switch, just ungrouped layers) it slowed AS down so much it was unusable. It took several seconds to select and deselect points. Moving points was slow and very choppy. It would be extremely frustrating to use with that set up.
The good news however, is that putting those layers inside a switch or turning them all off but the few you are editiing increased performance back to normal. Just as fast as if there was one layer. If that many layers are all visible AS slows down a lot. If only a few layers are visible then the speed increases. This is something to consider for onionskin. Onionskin is a real performance hog.
Another slow down occurs when keying a layer in a switch layer. It took several seconds on my PC waiting for the key frame to be inserted. Hopefully a scripted solution might be faster but it's hard to say without testing.
Playback also suffered dramatically. Forget about real time play back with that many layers in a switch. Scrubbing was very slow as well. Very sluggish.
800 "frames" or layers is small beans. In reality even a short segment might be 2 or even 3 times that amount. Maybe more.
File Size
My test file with 800 layers in a switch and a modest vector layer was over 50mb! You could easily end up with AS files 100's of megabytes in size. My test file was just a simple face on one layer. Not many points. Points in vector layers add tremendously to the file size. Imagine the resources required to have a 200 or 300 megabyte file open in AS.
Time Line/Frame/Layer Navigation
Now here's another wrinkle... time line navigation and editing. This I think would have to be handled with a new tool. You would need a way to automatically "select" the switch layer that is active on that frame. I tried to find a layer in the switch with 800 layers.... yikes!!! Scrolling and scrolling. This will need a special button or tool to select the active layer on a frame. Maybe as you scrub through the time line the layer is selected. Of course this means the switch layer with 800 layers will have to be open.
Another issue was right clicking on the switch to see which layer is selected... or to change it. ALL those layers are visible in the drop down box. So if the screen is not large enough or the layer palette isn't expanded to show them all they get cut off and you can't see all the layers. This is not an issue for a scripted solution since you would probably never want to right click on the switch anyway. You could use the frame number to know which layer it is but... if you change things along the way the layer numbering will be hard to fix.
From your description it sounds like a good idea to start with creating layers OUTSIDE of a switch and then use a script to load them in. However this will need to be done in "batches" so you can "hide" layers and improve performance. From what I've seen in testing this it may take a very long time to put 800 layers into a switch and key frame them. It took nearly 3 to 4 seconds just to set a new switch key.
Layer Editing and changes.
First off using this technique eliminates any possibility of using multiple layers for a single character. Unless you try to have multiple switch layers.... aaaaahhhhhhggggg! I don't even want to think about that

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Suppose you need to add new frames or make changes? This could involve changing keys for the switch in large batches. You must also rename the layers so they match the frame number. That should be an easy script function. I think this would be a must have feature. If you are on frame 0 and want to change frame 456 you just select it.
Also, will layers/frames be edited or modified on frame 0 or the frame the appear? This would need to be part of the script possibly. A special point tool that doesn't key on the frame but keys on frame 0. This is easy enough to do. You drag points on frame 489 but the special tool only modifies the points on frame 0.
File saving - Wait for the file to be saved!
A new wrinkle I just discovered... saving the file. AS has little "feedback" during a save. It's hard to see when it's done.
Normally this is not a problem, however I think I discovered what causes those corrupted files people have been getting every so often...
I hit save on my 800 layer file and it took... uh... it took a while. It took so long I wasn't sure if it was finished and I started clicking around on the file before it was actually finished. Later while the file was still open, I checked it on the hard drive and it was only 3mb.
This means it hadn't saved properly. My "clicking" or other activity must have aborted the save and squashed the file. I went back and saved again... waited at least 15 to 20 seconds before the cursor became "active". The file size on the hard drive went back to 50mb which was the original saved file size.
That size by the way is proportional to the number of frames. 400 layers in my document was 25mb. Double those layers/frames it is 50mb etc etc. A 1200 frame animation would be 75mb
In Conclusion - I'm a pessimist
Don't let me put you off the idea. I only did this so you don't end up being disappointed by unrealistic expectations. Obviously a better computer than mine will have better performance.
I would however, DEFINITELY do some tests to find out what AS can handle as far as layer count. Find the maximum number of layers in a switch that AS can handle without a performance or file size hit.
-vern