The following are my top two flaws of the Kohan series. While I don’t know exactly what happened to Timegate, I also suspect that the fact they were not fixed by the time KoW was released is a significant reason Timegate is no longer in business today.
#2: A greatly appreciated feature which distinguished the Kohan series from other RTS games was the random map generator. However, components in settlements were so effective regardless of location that they largely insulated the economic aspects of the game from the random map. To overcome this, they could have made the mines a lot more effective, and components a lot less effective. Alternatively, they could have made the map more like a Civilization map, so that the resource icons near a settlement are the resources that settlement gets, period (implemented well enough, they could also have used this to give players sufficient reasons to place settlements non-equidistantly from each other, instead of forcing players to do so by having only predetermined, random settlement locations, which would have reduced a lot of complaining about Kings of War as well).
#1: Perhaps the most touted distinction of the Kohan series was that it reduced micromanagement compared to other RTS games. While this can be considered largely true for single-player, for multi-player, it actually increased micromanagement, because there was always someone willing to increase the risk of getting carpal tunnel syndrome by constantly moving and clicking between the map and the retreat button (or using the hotkey) so they could individually retreat their companies into enemy ZOC tiles during combat, basically using the retreat command to maneuver freely within the combat zone, and to great effect. A simple fix to this, one which would have made the retreat command more what players rightly would have expected it to be in the first place, would have been to make retreat possible only into a friendly ZOS tile which both did not contain an enemy ZOC, and was not under siege (and maybe keeping a delay of some kind between retreat commands to the same company).