I hear ya, I'm sick of micromanaging the pollution clean-up. I just want a way to edit it or remove it completely, and I can't find anythign in the editor that would eliminate pollution (you can make buildings create 0 pollution but the buildings arent the problem, its the population)
And about your editor problem. I have the same thing... apparently they are working on it, but for now, create a backup of your civ3mod.bic file, then edit that file instead of creating a new one. (this file is the basic civ3 rules). So when you make changes to the rules in tha file, you wont need to play off a scenario, just play normally, and you should'nt have those advisor problems.