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Some things that really bug me.
1) We should have some control over terrain. Many armies, like Thracian, Netherlands, Carthaginian, and some Germanic were optimized to work in their home territory and don't work well in a different one. The TT system for picking terrain was slow and complicated; a lot of players didn't like it. But maybe some system where the defender gets to pick what terrain the battle is in (desert, farm, forest hill, etc.) Or maybe charge more for a legendary C in C and the best C in C picks where the battle is (assume he or she maneuvered the enemy into where he wanted to fight.)
2) I read a lot of history, and, unless there was a breakthrough, the lines would stay intact. The whole line would push ahead or fall back. Especially in cavalry battles, FOG fights end up in a confused mess. Some units are pushed back, others advance, some evade, others fall back. What historically was a linear battle always devolves into chaos. If a unit is part of a line, the whole line should bow back rather than having one unit back up out of line. It's not just that it's unhistorical, it also makes for headaches during play.
3) The player should have some say in if a until evades. For example, I am really tired of my Thracian Peltasts with shield, better weapon, better armor, and 50% swordsman evading a charge from a unshielded archer unit giving up that difficult terrain I wanted to control. Or not evading when a warband charges them in the open. If it's too complicated for the player to choose each time a cavalry or Lights is charged, make it so that units will not evade if they have a better chance of winning than the enemy.
4) Speaking of light units, heavy inf and cav have to either charge and risk pursuing light units into the middle of the enemy, or sit and do nothing. NO unit should pursue more than it's normal move after LI, especially disciplined units (Trained in the TT version). Or they should be able to "push back" lights without having to declare a charge. like in the TT version.
5) I would love it if we could order cav and medium units to perform "fake retreats" like was often done by many armies: Normans, Huns, Mongols, Turks, Arab conquest, Lithuanians, Parthians, basically every primarily Cav army.