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As the #1 messy coder around (and not that much skilled), I understand your complaints. I'm focused on Photoshop only, and the panel guide for CS4 was more than enough. My learning curve with CS SDK is, to put it mildly, steep (since I've not really any previous experience with Flex - and I agree, using 3.4 SDK and not 4.0 may lead to some confusion), but I'm optimistically confident that CS SDK for CS6 will be far more usable.
I find particularly annoying that to make life easier Adobe created CS Extension Builder, but to get it is nearly impossible (at least for me: I don't know if Gmail can't get thru Adobe mail server spam control, but in the last 4 months I wrote several emails to Roger Risdal, the "Partner Product and Business Developer Manager" in order to get info about the developer partnership required, and I got as the only answer a couple of out-of-office autoreply) Rumors say that Adobe's DevNet will undergo some robust changes (when, I don't know) - I hope they will change their mind about the way Extension Builder will be (or not be) distributed.
One last optimistic consideration is that the tools needed to deploy an extension (the ucf.jar for instance) and the general workflow (write the manifest.xml, pack everything with that java command line utility into a zip-like file, the .zxp, then write an .mxi to access features like auto-update and re-pack again into *another* .zxp) are far from having a good usability and being straightforward... so far that in my opinion the newer releases will surely be better than this one.
That said, I understand that experienced developers are happily plunging into CS SDK while I'm having hard times keeping my head above waters, and I'm sure CS SDK will lead to a very interesting future.
By the way, to drop the SWF in the panel's folder isn't a good idea if you want the extension to have the right dimensions (this is something I've learnt) - the manifest.xml is the right place.
Yes, Adobe people read most if not every forum post concerning the SDK.
Most of the bullet points in your post are covered in this document:
As for the code itself, Ole wrote a fine cookbook entry on moving from PatchPanel to CS5 Extensions,
Rest assured that we reading your comments and will do everything we can to help you be successful.
Oh, and Davide's posting with the eval example is what you're looking for on that front.