Okay here's my tips so far. Most of this is probably common sense or something you have thought of as well, but anyway...
1. Because of the limited eras of you mod, I think you can get away with letting them use the standard tech tree and only using 2-4 land units, and 1-2 sea units. You could always use more, but I think this is a good minimum.
2. Make their units not require resources.
3. You can use custom player data to make them unselectable for the human at the civ selection screen, yet still exist as an AI controlled opponent in-game. However this might cause playing aid mods such as Civ-Assist and MapStat to not work, but I'm not completely sure about this (need to test again). On the other hand, someone might want to play as a single city civ for the challenge.
4. I like the idea of them having one big, strong city, so consider giving the minor civs their own little "super building" (gained through the "minor civs tech" you mentioned) that allows them to compete a little bit by increasing production, defense, science, gold, or whatever is appropriate. Give it culture per turn if you want it to be destroyed on capture, or "Allows city size 2," if you want it to have a good chance at being intact when the city is captured.
5. Something I'm considering is having the mutual protection pacts and military alliances only be attainable through diplomacy with minor civs. This way you might want a few important little allies, rather than simply gunning to take over their nice cities. Again, gained through, "minor civs tech."
6. I should have asked how many civs will be in a single game as well. If you're doing a preplaced map, there's no problems, however my problem has been that on random continent maps, sometimes a civ will start surrounded by minor civs (giving them too much room), and the other major civs are near each other as well (making them relatively scrunched together). It's not as much as an issue on pangaea or archipelago maps, but bothersome on continents. Messing with the ratios of major to minor civs in a game might help some.