I suggest reading some of this
CC thread. The guys at Campaign Creations are all about campaigns, so chances are they will be able to provide you with a
lot of insight for campaign-building.
Being a pretty veteran group and having some people that are really grumpy over SC2's editor and shit (issues like the transitions), a few will probably tell you to just give it up; take their words with a grain of salt and persist.
In all seriousness, the old folk at Campaign Creations are pros at campaigning.
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For the sake of story-telling, just scrap the whole idea of choices. At the end of the day, they're a gimmick. Those stupid choose-your-own-adventure books? Self-evidently
stupid. If you're going to do a "choice" map, I strongly recommend following with Blizzard's implementation in the Enslavers SC1 campaign, and doing only such a gimmick at the end of the campaign or very near to one.
Save your own soul and avoid branches within branches. It works in visual novels and shit, but not for something as consuming as an entire campaign (unless you just feel like taking the challenge, I guess).
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I think you should forgo hosting campaigns over Battle.Net. For the most part, campaigns are single-player anyway, so you don't need an active hosting service like B.Net. Not only that, but Blizzard has censoring policies as dumb as a scrotum of bricks, and the size limitations don't help.
At this point in time, hosting campaigns over Battle.Net is severely inferior to uploading to a site like StarEdit.Net, which has the added advantage of having a forum for people to actively discuss and critique your work (and even advertise/endorse it!).