I agree, that the current system does not reward bigger and older cities to a sufficient degree. You indeed only need one and the rest offers only a marginal benefit in the form of another multiplier ... if the city produces gold or research points.
However, I also have a strong negative opinion to some aspects that are commonly used to avoid city spam, some of your suggestions in particular or city spam avoidance at all cost in general. Let me explain:
a) The various forms of maintenance cost / corruption or whatever based on city numbers or distance from capital should not penalize success. If I want to conquer the world, which is a legitimate way of ending the game, I should be able to do so without running my empire into an economic meltdown (as e.g. happened with CIV III corruption increase) or having to raze all new cities. Where's the fun in that? The AI should be the challenge, not preventing your empire from imploding while kicking its butt.
b ) The "everybody gangs up on you" solution? I always hated that. What your advocating is essentially the way diplomacy is based on in most 4x games. They can have been your best buddies, be flies beneath the marching feet of your soldiers, have no chance of success at all ... if you reach a critical mass everybody just declares war on you, no explanation given, no previous history taken into account. One algorithm simply takes over. Do you have Lichtenstein declare war on the US because they are the (self-proclaimed) only super-power remaining? No. Sometimes people stick around the big guys.
And long story short you would just again penalize one way of winning the game (i.e. the diplomacy victory) while at the same time being efficient and running a large empire. To get back to my far fetched example. Not only Lichtenstein should be able to achieve a diplomatic victory, the USA should be as well.
c) Monsters aren't a solution. As the game stands now, they are already a bigger threat and more demanding opponent than the AI. And that's not what at least I expect from a strategy game. I want to play against a cunning AI, not a mindless and never-ending spawn of monsters. They should be a nuisance, but not the biggest threat out there. And lets face it: monsters and the possibility to contain them thus are probably the biggest reason behind people spamming cities right now anyway.
d) I agree, that expanding your empire should also come at a cost. And some games found a more or less elegant solution for this e.g. like CIV IV or - just look at your avatar - even the MOO3 with its overhead. Both of the games also offered technologies or buildings that help you reduce these costs to some degree (which are a MUST in my opinion as it allows the player to tackle these negative effects and not just be a victim to them) and could be modded to get rid of them, if that didn't fit your idea what's fun. Yes, some people actually LIKE city spamming. Don't just punish them, because you dislike it.
e) With more expensive pioneers you have to be very careful not to slow down the pace of the game in the beginning to a crawl. I seriously would not enjoy it e.g. to have to hope for lucky goodie huts, not build anything else or spam the end turn button so often just to save enough gold for my first or second pioneer.
All in all, one should be careful with the tools to limit city spam and not accidentally penalize players for playing while effectively and efficiently wanting to expand their empires. Not everybody likes playing a city state ... and most historic ones where not really happy only being a city state either. *evil grin*
Rabenhoff
EDIT: Is there some way to turn auto-smilies off?
EDIT2: Made a new post instead of the edit as it got bigger and bigger.