A #2 from me.

I absolutely loved playing the battles, loved it even more with the mods.

My main gripes are, turning units (I can't number the times I did the old alt-rightclick) and the speed of the units, but I don't especially love the routing flags (too obvious).

In general I get the feeling that I just need to adapt, at least that is my initial thought.
I have been in a semi-hibernation and haven't noticed what people either complain about or love all too much. But I have noticed a few comments on the dragging of a line of units. I haven't had much problems there, I acutually found it very similar to the MTW experience. It was perfect for th modded tutorial battle where you play the main Roman army. I just loved to line my Principes up right behind my Hastati who in turn where behind the Velites.