Instead of having one speed limit for all thrusters every tier has it's own limit. This would be a great way to encourage people to build better thrusters. Moreover this would make the game more realistic, because it's unrealistic how a tiny low tier thruster can propel your ship to the same speed as a big high tier thruster.

I am not sure if this is possible with the current modding support, but it might work through scripting: Once a thruster's speed limit is reached the thruster's force is set to 0 or it is simply shut down. When the speed sinks below the limit the thruster applies a force again.