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For a Flash-based design I would go with option 3. The general controls and objects common for use with each activity would be in the main file. Whether or not the main file would be responsible for sending activity data to the server could depend on there being determinable similarities between data collections... otherwise it might fall on individual activity swfs to interact with the database. There are too many unknowns in this regard for me to offer much.
If this was going to be a loaded application, such as an AIR app, then option 1 might be more reasonable since you only have to install once for everything to be available.
When it comes to mobile you are likely to hit a snag if you rely on using AIR/Flash to try to deal with a main and activity swfs approach... mainly in the Apple realm... unless I forgot a lot of what I was involved with some time ago, a loaded swf cannot contain any code when it comes to iStuff. So you end up having to make the main file contain all of the coding to deal with each activity's processing. Every interface/interactive element can only exist by name and the main file has to target them and assign listeners and processing and etc....a mess in my view. That's why having the one huge AIR file is possibly a tad more reasonable.
Thanks so much for the thorough response, Ned! It's especially helpful to know about the concerns with AIR.
I consider them concerns with Apple myself... they are costing me a career.