So I too don't really care for the length of some of these scenes for SH. I normally don't mind because it's just a part of the actual full episode, so they're linked together anyway to make the 20-30 minute version that I host on my site.
I split the Acts up into scenes for the following reasons:
1)16,000 frame limitations. I will usually go past this. Actually, I know for a fact that I will.
2) The earlier episodes were attempted to be done in one flash, but even with optimizing, the file size was still huge, over 200mb, and trying to edit it in using Flash which whores up memory regardless of how good my computer is becomes a hassle and extremely frustrating. So to prevent that annoyance, I do separate flash files, much to my own dismay in order to keep myself sane.
3) I split the scripts into "fading in" and "fading out" to signify what should be able to fit in the Flash file without having to stop to start another one. So when a smaller scene is followed by a big one, I keep them separate instead of making 2 files that are relatively long.
4) It's just convienent when I want to adjust something at a later date.
Now, for the full episodes I link the swfs together with Actionscript. It works out pretty damn well. However, I don't know how I'd be able to put out a full episode on NG, one with the file size limit and as well as the fact that each scene is in a different flash. I'm sure I can try and figure something out, maybe just push it and put two scenes together.
Until then, all full episodes can be found at www.azure-productions.com