I think the Order are a pretty great species so far, but I’ve had difficulty diversifying with their designs - ultimately most of them end up being slow, heavily protected long-range ships. I use the Crusader Cruiser and Spirit Frigate as fast-attack, close range ships given their low speed penalties.
I use the Temple as my mainline long-range cruiser, with the Priest going purely long range with an EMP beam and the Trinity as a carrier and anti-fighter platform with limpets and defence lasers.
Has anyone discovered unique uses for certain cruisers? I find mine tend to just clump up in a line and blast away.