The strategies dealing with careless city expansion would include 1) take the city and keep it, 2) take the city and destroy it, if size 2 take settler, 3) threaten the city and draw more of your troops to defend it, then either send even more troops or move the troops away and attack elsewhere.
Going to take a long time if the opponent has 50 cities. In the meanwhile the other 49 will still produce resources. Yes, I expect many cities to change allegiance during the game. But with excess cities, that's not really an issue if you just loose a few..
Most things that apply in SP will also apply in MP
Exactly. That's why I think it would be best if any changes which will be done to balance MP will be added to SP beforehand for a thorough testing of the playerbase... Allowing MP to start with the least hassle.
What happens if you hit the limit and then want to capture another city?
It will be razed upon capture. Want to prevent that? Raze one of your own before-hand.
what happens when you have a quest to settle a new city or you need to build a temple to a god?
You'll have to sacrifice one of your cities if you want to complete it. Although temple might be done without if you have a spare holy spot.
Say max of 35 cities per player for the whole game or does it only hold up to turn 100?
Whatever the host set it to be. And everyone has to agree before the game starts...
(I hadn't even thought about allowing the option to expand the max the further the game processes. That's a good idea!)
What happens if one player wants a max of 30 and another wants 50?
You'll have to make an agreement before the game. Just like you would need to do with your negotiations with other players. Only with a lock, you can be sure it's held up, instead of finding out in turn 150 one player suddenly has more. Maybe not even noticing (gone over by capturing a city for example).
Also; settlers can still be constructed and send out as desired, only if the limit is reached they cannot construct their city. Handy for backups if one of your cities gets captured for example...
Most players are honest and will stick to houserules.
I don't share your faith in humanity I suppose. Also it would be really hard to manually keep to a limit of 100, since there is no real easy way to overview the amount of cities you possess. I suppose in both systems such needs to be added.
Those that don't will soon pick up a bad reputation.
New players can hardly know reputations. And scaring them off with several bad MP-experiences would be, well... bad.