Ah, I'm afraid that there's no way to change teams, factions, maps, etc; nor any way to "save" the resources and units in a scenario to pass into another,
but there's no reason to believe such features won't appear in the future. Lua can create units, resources, upgrades, make timers, recognize when units enter an area, give units commands such as to attack, create messages and display text, etc. GAE has advanced methods of moving the camera and freezing input to allow cutscenes, as well as the ability to make coloured dialouge messages in the console akin to messages from other players.
if you look at some mods like Apocalyptic Dawn(which hopefully version 3.0 will be released soon) There are much more advanced scenarios.
Apocalyptic Dawn v2.5 (last released version) boasted over 20 scripted scenarios, some as simple as just giving a different style of gameplay (eg, king of the hill requires you to hold a position for 20 minutes), some modifying the starting units to allow games to start with full bases, etc, and the "campaign" of that version, a five scenario story-based campaign called "End of Mourning", where the player leads a betrayed army to discover what happened; even ending with Glest's first and so far only "boss" battle.
Of course, v2.5 was fairly rough, and the
planned version 3 has a load of improvements in store...but it's not to be released "soon". In fact, between school, work, sports, and all; I haven't worked on it since, erm, the summer. By no means abandoned, but no time at the moment.
Also, moved this discussion to a new thread.