You say that sieges don't really work, but they do. I know because I use them all the time and I have broken even the strongest of civs. When it comes to civ1, quantity always beats out quality, in my experience. I think it's because you are giving the AI too much credit. They are not very good at using their units, responding to threats, defending their cities, attacking yours, or mananaging ANY aspect of their military. Here are a few examples:
1. The rock. This is actually a documented strategy. When you find a computer civ, find a mountain or other fortifiable spot near their capital. Make peace with them first to buy you some time, of course. Place a phalanx on the mountain and fortify it. The phalanx should now have about 10 defense or so (depends on whether it was veteran or not). You can even build a fort and put two phalanxes in it. This little fortress of yours is basically impenetrable, but who would WANT to take it? Apparently, the AI thinks any military that close to its capital is a threat, and once the computer chooses a target, it doesn't stop until it takes it. In one game, I did this to a civ that had 3 cities. 2000 years later, they still had 3 cities (roughly the same size), the same amount of tech, they were still at war with me, and neither fortified phalanx had been injured.
2. Attack/defense. The following is the best defense strategy for a city that is under heavy attack... Build city walls. Place 4 good defensive units in the city and fortify them. Get 2 counter-attack units (one fast and one powerful... ie chariot and catapult) and sentry them in the city. If an enemy unit gets within one square of the city and stops, kill it. Make sure to use the more powerful unit if you are attacking a unit which is, by nature, a defensive unit (such as a phalanx). Now, there is a good counter to this. The key is to get about 8 1-mp defensive units (militia and phalanxes). Bring along your other units as well, whatever you have, legions, catapults, chariots, cavalry. Now move your units into a ring around the city so they are all two squares away (exactly one empty square between them and the city). Once they are in position, move your defensive units into closer range, all at once. Your opponent cannot destroy them ALL... If you have legions, move them onto squares captured by phalanxes in this turn. In the next turn, fortify any that survive and wait. In the next turn, your opponent will kill off all of his counter-attack units. Now it's time for you to either fill in the gaps to complete the seige, or move your chariots and catapults in for the kill, your choice. Now to the example (finally)... I was on a continent adjacent to a powerful enemy (the english). They were constantly landing on my shores and capturing my weaker cities. I was managing to keep them from permenantly taking anything, but the war was costly. So, I saved up and filled a frigate with some good attack units and sent it off to their continent. I took a city of theirs which was positioned in a flatlands area (no mountains etc nearby). I set up 4 phalanxes, a chariot and a catapult as defense and bought city walls. The English stopped all raids against my coast and concentrated on capturing this new city of mine. Having no concept of strategy or tactics, the English tried again and again the same failed ideas. Over the next couple hundred turns of the game, as I built up the population, military power, and technology of my civilization, the English attacked and attacked this city. In that period, I had to replace 2 phalanxes that got killed. TWO! The English had lost over 200 units trying to take the city, and had not gained an inch.
So my point is the AI is stupid. Using strong and powerful defense on all of your cities is just too expensive and inefficient for defeating them. If you feel threatened by an enemy civ, don't you dare tuck your tail between your legs and brace for the attack. Instead, find out what makes them tick and defend just ONE city well, or attack just in a certain place... Keep your eyes peeled and you can't lose.
Now, you mentioned that there would be a problem with defending oneself against a strong attack in the 1 size-6 vs 3 size-4 match. If you are the 3 size-4 civ, there are several ways to combat this. The best one is packing your cities tighter. Yes, there will be overlap. But remember they are only size 4, and if you are playing a militaristic strategy, then they may stay that way for a long time. The overlap could cause problems in the endgame when you want to develop those cities, but some can always be destroyed. These tiny cities are a dime a dozen. Keeping them close allows military units to move quickly from city to city, makes creating roads easier, and if you feel lucky you can just defend the ones on the outside ring and leave the inner ones empty! Trust me, the AI is too stupid to sneak past your lines.
Here's something else, that may help you in the midfield battles... Called a lockdown. Generally you will try to spread your units out as the cover the ground between your cities and those of your enemies, and if there is a steady flow of them, they will look like a scattered grid of units covering the landscape. If a tank, chariot, or other dangerous unit should kill a unit at the edge of this grid, it is time to "lock down" the army. For units which are close to the dangerous unit, fortify them immediately wherever they are; fortifying takes a turn to take effect, so you need to start now. For the units which are a few turns away, move them onto the best nearby terrain and fortify them there. If you have offensive units like cavalry, legions, and chariots, retreat them so that they lie behind the fortified units and your enemy must move through your lines of CHEAP (remember that!) militia and phalanxes to get to them. If you have catapults, try to move them onto spots where they are in slowing terrain, so that enemy units must move one square at a time to get to them. This gives you the option either of out-running the faster unit, or simply waiting for it and striking when it gets close. If you follow these tips, the dangerous unit will be dead before it's bagged it's first legion, I'm serious. In battle, think of your units in terms of their economic value; sacrifice 3 militia before you let your chariot be touched, etc. and you will often be pleasantly surprised when the tank attacking your fortified militia DIES.
Another thing you can use to your advantage in such a scenario as you described is targetting the settlers. Use your cavalry and chariots for wiping out your opponent's settlers (which are out building roads and irrigation, often unescorted). Whereas your settlers became cities long ago that are now well defended, your opponent's settlers are all over the place. And these settlers are more than just a unit. They are more than just 4 times the cost of a militia. They are are more, even than 1 population point. What they are is the future of your opponent's civilization. He will rebuild and rebuild them, trying not to fall behind in the race for population growth, while his economic, industrial, and population growth are continually being stunted.
Most importantly, in conclusion, I must say that when playing the 3 size-4 cities civ, surviving itself is more valuable than you could ever believe. With fast population growth maintained over a long period of time you will soon reach that state of monstrous size and power so as to be untouchable by all other civs. I can remember my armies touching shore on the coast of a new nation only to find that my soldiers outnumbered the civilians of the opposing civ (I had about 160 units in the initial wave of attackers). Or when a tank threatens your lines and you find that it kills 8 units and when it is finally destroyed, your lines have advanced anyway in spite of it because you are so powerful that it did not even slow you down. You have the potential of creating an unstoppable fighting force, so don't give up this chance. Keep fighting!
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