My giant list of suggestions
I find 1, 3, 4 very important to make warfare mods better. In fact, I can assure you that if they are implemented in some way, warfare games would get so much better and only slightly more complicated. The other three suggestions are just things I personally would like to see but I don't think everyone would agree with me.
1. Directional fortificaton(most important for me) So far I have yet to see anyone implement or even suggest this but it has sooo much potential value and I'm sure some of the better modders can make it. Basically it's just choosing a direction to fortify in, per se, a 50% defense bonus in that directon . However, attacks on the side (i.e. flanking) gets a good bonus. This is to make lines of defense (i.e. the maginot line) have some value, even if it is not alot (and yes I know the maginot line failed). To me, merely fortifying cities with troops is stupid and unrealistic because in conventional wars, most battles are fought outside cities, and with the current design of Civ 4 almost none are. Also, for units that just used up all the movement points, they can pick the direction they're facing for no bonus but attacks on the flanks still are devastating, as they are in real life. To protect flanks, they're should also be a "protect flanks" forification (but now movement points are required) wherein you get a 25% bonus when enmies attack from the flank. Note: the flank is always determined by which way the other units are facing so, for example, if your units are facing left guarding the flanks protects units coming due north or due south.
2. Realistic Movement During war time, travel on any type of road is 1/2 of a movement point, regardless if it is in enemy territory. If you think about it, why should traveling on a railroad be so much faster than traveling on a road if the unit is motorized? In real life, troops move just as fast, provided that there is no enemy resitance, in their own territory as in the enemy's. This restriction gives an advantage to the attacker and allows the attacker to sustain a breakthrough.
3. Military Control During war, once your unit occupies a plot of land it is yours until the other countries unit reoccupies it, even if your unit has moved because in real life a division leaves a small amount of troops in areas it conquered to control the population, small enough so that it doesn't affect the force of the original division or pose a threat to an enemy division. This way you can set up supply lines and can cut off enemy supply lines.
4. Supply Lines Combined with my third point, it can make supply lines a very important concept in the game. All units have a supply line that connects them to their home country. However, if the unit is surounded by enemy territory, which normally couldn't happen without suggestion 3 implemented, the line is cut off. Each unit would have a supply of amunition and mechanical units have a supply of gasoline (I believe there is already a mod for this so it would not be very hard to implement). The use of ammunition is determined by how much the unit fights and gasoline consumption is determned by movement. One they run out of ammuntion they die and when a motorized unit runs out of fuel it can't move.
5. Fortifications and Military Bases There should be new fortifications like pillboxes or other things that give units fortified more bonuses. Permanant artillery should also be available. Also, there should be an option to make something called a military base that requires takes a very long time for workers to make. It can hold aircraft and can be named, and function much like cities except there is no population, it cant make things, and has no cultural influence. You name them and you can also trade them in diplomacy. I think someone already has done this but I'm not sure.
6. Specialized Units Basically I'm tired of one unit dominating the game because there is no adequate counter. Instead I propose eliminating all specialized types of infantry (marines, paratroopers, etc) for just one you make. Once you make an infantry unit, you get to pick its "specialty", which is just a big promotion, not the uber horsehockey one you get now. For example, you can make an infantry an anti-tank infantry by a promotion that makes it 50% better against tanks. You can also have promotions to make it a paratrooper, marine, etc. However, each unit can only choose from ONE of the specializations. This eliminates the need to have a bunch of different infantry and still have flexibility.