Perhaps the hardest thing for wargames to replicate (aside from the fear of death, naturally) are the problems of command and control. By nature the little cardboard counters, blocks or toy soldiers do as they are told. Where they are is generally pretty clear and their overall status known.
In addition, the wargamer has a bird's eye or map's eye view of the action in real time.
This isn't too big a problem for 20th and 21st Century wargames, outside the very tactical level. Even fairly low-level commanders at battalion and regimental levels are often fighting their battles on the map, as it were. The modern battlefield is often far too expansive for anyone other than a company commander to see his whole fight. At sea and in the air the same is true. The captain fights his ship from the computer screens in the Combat Information Center, not from the salt-sprayed bridge. The fighter pilot relies on his head-up display at least as much as his eyes.
Even in the black powder era, top level commanders were familiar with maps and probably imagined their battle plans from that perspective, although exercising anything other than the most general command was difficult. A lot depends on the man on the spot. The problems of command at sea were similar, with flag signals being a very crude level of control, barely adequate with the stately pace of sailing warships and breaking down completely under the quickened pace of steamships. The wireless set came not a moment too soon.
But in ancient times maps were few and crude and there's little evidence they were used much by leaders. Everything was seen from ground level. There's not a lot of evidence for exactly how commands were transmitted, but couriers, musical instruments and visual signals were probably used.
War Galley makes stab at reflecting the problems of command control, and deserves kudos for the attempt, but battles in the game system usually degenerate into a confused melee. This is a problem in other games, too such as the age of sail wargame Close Action.
The wargamer, able to look down from above, is much more aware of the tactical possibilities than any real-life captain could have been from his sea-level vantage point. The turn-based temporal system of wargames also provides opportunities that wouldn't occur in the swirling midst of battle.
In any era, the thing commanders fear most of all is disorder, but this fear was particularly salient in earlier times. In ancient warfare the first army or fleet to fall into disorder was usually defeated and in the wake of defeat the slaughter would begin.
It's unreasonable to ask gamers in the heat of battle to forgo tactical advantages, but there needs to be a greater incentive for keeping formation. Perhaps all ships not facing the same way as the flagship should be considered "independent squadrons." It's hard to imagine a squadron commander coordinating the actions of a dozen triremes in the middle of a melee from the deck of his own ship that's busy dodging rams.