I'm not familiar with those games, but it seems to me that there ought to be a way to simply link adjacent units so that they act as a screen and move together as such. Likewise, great generals need to be attachable in some fashion. That they just move around and get caught helpless is insane.
AI does a lot of insane, like use GP's for reconaissance. Personally, I'd like to think that Leornardo da Vinci has better things he could be doing.
That seems like something that could have been coded out easily enough.
Warning: long post ahead. I tried to keep it short, but I've failed.
I'll elaborate a little on these ideas, for those who might be interested: in many Paradox and AGEod games, there are a maximum number of units that can be committed in any single battle, usually determined by technology and terrain. All units fight together, so you order one attack with a stack against another power's stack, taking into account terrain modifiers, rivers, commanding officers, etc. Instead of fighting until the utter destruction of a unit like in Civ4, it is common to have battles where both sides survive (this is done by tracking organization and strength separately). Units are destroyed when they run out of strength, and retreat with reduced strength when they run out of organization.
What I would like to see is some evolution of an OOB (order of battle) as the game progresses. At first, you produce units that move and fight individually, much like Civ4. Then, army organization can be researched that allows you to group several units into a single army, and you'll get some bonus for doing so. As an example, 4 units grouped into an army will fight more effectively than 4 independent units (combined arms). As the Renaissance and Industrial eras come, you can research divisional organization, to increase the number of units you can attach together, and corps organization, which acts as an intermediate between armies and smaller units. Corps will support other corps of the same army in neighboring tiles (march to the sound of the guns).
Thus, in the Industrial and Modern eras, you might have one army on a short border, which has three corps. Each corps has maybe 5-9ish riflemen and grenadiers, a couple cavalry, and a couple artillery units. You might have a couple free cavalry units for scouting as well. So, despite having several "units", you are only moving maybe 5 combined units on this front. On longer borders or against major powers, you might have 4 or 5 armies in operation, each one consisting of a few corps. Thus, even in a large war, you might not have more then 20 combined units to move around on the map, but they are comprised of maybe 100 or so individual units.
A couple other ideas that work with this are replacements and more generals. It has always bugged me in Civ that the victor in a battle doesn't have to pay any additional production to replenish his unit, it only takes time. Thus, I would suggest at least a Paradox-style manpower system, where your units will only replenish strength if you have sufficient replacements available. Obsolete units could be turned into replacements (which would solve the "upgrades too expensive!" problem), or you could build replacements in your cities.
Finally, I say ditch the concept of great generals as currently implemented in Civ. Instead, your nation gains leadership points, which you use to buy generals to lead your troops that have random attributes (bonuses to troop morale, movement, attack, defense, quicker sieges, org. regain, war weariness reduction) based on your nation's military traditions. If you have national wonders like the Heroic Epic, West Point, or Military Academies, or tons of accumulated experience in wars, you get better generals. Then, you pick which generals you want to assign to each front (i.e. I want guys good on defense to guard this mountain pass, while I want a fast and aggressive general to lead the army attacking X city). Generals would be automatically retired after so many years.
This might sound like a complicated system, but with a proper GUI, where you could see the maximum frontage in each tile in a popup with the production, where you have just a handful of buttons to add or subtract sub-units to your corps/armies, and your current manpower reserves are shown on a counter on the main screen right next to your science bar, it would be easy to keep track of all the relevant information. Plus, since the OOB develops gradually over the course of the game, it will not overwhelm new players, and it will allow them to learn the system as the game progresses.