Joining the thread late in the day...
Things to keep:
Turn based WEGO system
For me it's the perfect mix of being able to make your plans in your own time, and set everything up, while still giving the exictement of seeing things evolve in real time
The interface
Obviously it will need changes and refinements to work with the new engine, but the basics of the current system, with waypoints, targets, cover arcs is very easy to use and flexible enough that I very rarely find myself unable to get a unit to do what I want.
Things to change:
Convoying
Traffic management is a headache. Following a road should have low command delay overheads. Vehicles should be able to follow the one in front intelligently - queueing behind it without getting into the reverse/forwards traffic jam nightmare.
AI scripting in scenarios
Not full scripting, but the ability to tweak the AI's behaviour to make it fit in with what you want from the scenario. There are tools to do some of this - use of victory flags, reinforcement times and locations (to make the AI lead with infantry, for example), and various other tricks that scenario designers have come up with. But being able to inform the AI of key points to defend, which defenders should stay put, which should be ready to fall back, which are the counterattacking reserve force; all of these are useful tools that good designers could use to make scenarios significantly more challenging.
Campaigns
I suspect that anything even vaguely mentioning specifics would be wasted due to limitations imposed by the game engine design, but any kind of campaign is good in my book. Either the kind where you need to win a series of tactical fights to gain a strategic objective, or the kind where you have to keep your core of a battalion intact as it gains experience.
Better terrain system
More flexibility in laying out terrain, particularly with villages. The kind of closely packed streets and alleys you find in western europe simply can't be modelled with the current system that well.