[Phoenix-D]

"There is much more flexibility in such a system, allowing for more diversity in movement. With the big engines, you would get movement rates like 3, 6, 9, instead of anywhere between 1 and 9."

No. You make an engine that gives 1 MP, and make it, oh, 20000t. (the point is that it's too big to use).

Then you make a mount for each ship size, restrict it to only that ship size. It reduces the engine size to an appropriate number. It's just like standard SE4 movement (minus movement bonuses), only the engines themselves get bigger as the ships do.