The scenario editor sounds very limiting to me. However, sometime ago I had given some thought to using sequential function charts to keep track of and advance the story line. SFCs are a sort of generalized state machine that allow selective and parallel branching (parallel branch => simultaneous threads). I thought it could be done as a plugin that would provide signals (data and events) to the underlying AGS script. The idea is that one would be able to construct a game world complete with working characters, objects, etc. The plot elements, puzzles, game play would then be imposed upon the game world via logic contained in the SFC. See the examples below.
http://infosys.beckhoff.com/content/1033/tcplccontrol/Images/BILD5_17.gif
http://www.3s-software.com/index.shtml?en_v3_as
http://infosys.beckhoff.com/content/1033/tcplccontrol/Images/BILD5_17.gif
http://www.3s-software.com/index.shtml?en_v3_as