But all the rest of your suggestions, seems to indicate you really haven't explored all the filtering options. Most of the cluttering comes from the smaller features under the "Spot, Building, Farm" category, and there you have lots of sub-categories like churches, etc. you can turn on/off individually.
Same for the "Population" category, it has sub-categories so you can filter out the smaller towns.
I turned off more today and it helped some. Seems if I turn off Populated Place, it turns off names of pretty large towns as well as the intersections towns. Still, not the end of the world since larger towns have hospitals, railway stations, etc. that identify it. Still, some more control would be welcome.
Is color coding or smaller tagging a bad idea? In places that have a lot of things, if the tag was nothing more than a string at 100 AGL like FSDiscover does, you might be able to at least read the things. In most places you want to have a fair amount turned on but then you come into Monterey, San Francisco and places like that and you have two choices...either shut it off or change filters big time so you can read any of the tags. Honestly, as it is, I think I'd have to keep it turned off over any city.
EDIT: Here's a picture of Monterey with quite a lot turned off...
http://i.imgur.com/Dgpyy3n.jpg