Three things that are apparently not included but should be IMO:
1) setting up diplomacy/attitude options in the editor (i.e. this civ A is at peace and polite towards civ B who is at peace but furious with civ C). Locked alliances are only usefull in purely military confrontations but these less permanent changes would gave scenarios much more depth in reflecting historical enmities.
2) Setting builds (and shields accumulated) in cities.
3) Setting unit status (fortified, unfortified, moving etc). Less important than the other two suggestions but would be cool nonetheless.
hopefully some of these may be addressed in patches. The editor went a long way from the first Civ3 version to the one in 1.29f. so I have hope
Finally, this is a future suggestion on editors (i.e. Civ4): for Civ, doing a scenario is a process which is usually done in parts. Usually this involves 1) map, 2) cities, 3) improvements, 4) units, 5) global settings. What would be cool is if the editor was split into these parts so for example, you'd be in map mode and all the options for map making would be easily accessible (for example, icons for the terrain types and overlays), then you'd go into city mode with perhaps a window with individual city options, etc etc etc. As it stands, the editor is a bit clumsy in that it does everything at the same time and doesn't really make each part of the scenario-building process as smooth as it could be.