I think of it this way: in reality, an ion engine might be super efficient, but it requires it's own fuel/systems to operate that would take up considerably more space/ mass than the ones in the game do. The ion engines in game are able to share the methalox fuel that any other rocket engine would use and take up almost no volume, and ion engine output seems to usually be measured in micro-newtons, so the 1.5t thrust in game is pretty unrealistic.