Slow down the age progression:
In Age of Kings, it seems that the game is often a race to Imperial Age, then you fight. There is a massive defensive advantage in the earlier ages, which evolves to an attacker's advantage in the Imperial Age, especially with trebuchets. The attacker doesn't really have a chance until the Castle Age, regardless of how unprepared the defender is. Even if you expect good results, attacking before the Castle Age is rarely a good way to spend your resources at that point in the game. I'd like to see the ages last longer, and the conditions set so that earlier warfare is more common and practical. I assume AOE III will have 4 ages - I'd like to see the first 3 play a bigger role. If it's designed to be a 2-2:30 hour game, then a strong player should reach the final age at about say 1:30, not 45 minutes. You shouldn't be able to survive without a military by at least the 2nd age.
Default stance:
I prefer the defensive stance for most of my units. I'd like it if we could specify the default stance for any unit built at a given building. That way we don't have to find our new units and change their stances. You should be able to tell units to guard an object, or even a group of objects. If a distant artillery unit attacks a protected object, they should be smart enough to travel however far it takes and kill it.
Go back to AOK map sizes:
I personally don't like the "Normal/Large" map sizes in AOM. Both of them are smaller than I'd like, and I prefer being able to pick from a wide range of map sizes like we can in AOK. AOM scales the map size according to the number of players, but I prefer to do my own scaling according to my mood.
Separate the patches:
This really applies to AOM as well as AOE3. We all want to download bugfix patches when they come out, but not everyone likes the gameplay balance adjustments that come with them. Often it seems the balance issues are addressed by watering down all the texture in the game, rather than boosting counter-units, etc. Online multiplayer will always require that we use a patch with the latest accepted balance adjustments, but many of us don't play online, and in those cases I'd like to be able to opt-out of the balance updates while still getting the bugfixes and feature enhancements.