There are ways around this, and some funny things you can do with formation orders and such, but I think a very simple modification that would add a bit is “Adjust Speed”, so that we can purposefully slow down faster ships. This is primarily of importance if you use the same ships in more than one type of deployment or map – if you’re custom making ships for every deployment, than its not needed as such. But it can be annoying to swap out an engine just to lower the speed of a ship, and it feels a little bit cheap.
Plus, and perhaps more importantly, an “Adjust Speed” order can be given a conditional variable indicating when the ship should increase speed. (All orders should have more conditional variables, in my opinion.) For example, maybe the “Adjust Speed” order will only take effect until the ship engages the enemy (is fired on or fires on another ship). Or maybe there could be a slider to indicate time – the number of seconds to move at that reduced speed.
In some cases, the reduced speed could even be 0. I don’t know if I have as much of a problem with “engineless ships” if they actually have engines. Especially if there are conditions set under which the ship may move (or be moved).