Brilliant list of suggestions!
CaptureAge features would really help. I would especially favor its main feature (IMO) both while spectating and playing - displayed economical (villagers+fishing ships+trade units) and military population counts.
I also love updated sinking animations and there is a topic about it with screenshots.
Currently there is no way how to have corpses decay into skeletons, but you can have visible corpses if you want.
Seems to be a nice idea, but is it possible to add people with appropriate animations to siege engine graphics without making it look too crowded? Siege engines crews consisted of many people and it would be impossible to fit them all into graphics. 1 person might fit into graphics but can you imagine only 1 person operating a trebuchet? 
Hell yeah! It is my most wanted feature and would really make managing large armies much easier. Here I suggest how to implement this into UI.
Control groups would still be useful for managing army groups with different roles (melee, ranged, siege) in battle. Large selection limit would help when managing army as groups is currently not appropriate and player just wants to move large amount of units on the map.
Developer warned me about using it during beta, explaining that it causes pathfinding and collision errors.
I would also like to have:
- Possibility to totally disable AI kiting + projectile avoidance everywhere (standard game, campaigns, etc)
- Having specific cursor for out of range trebuchet targets or at least possibility to disable automatic trebuchet packing for such targets
- Farmers counted as food gatherers during building farms to avoid confusing fluctuations of food gatherer count