While you're at it, add an assimilation beam. You fire it at the enemy ship, and soak up (part of) their weapons, defenses, hit points, engines, and other systems, so they are now on your ship not theirs. After a while, there won't be a thing that could stop this ship.
Back to the point, yes, RTS tends to have the possibility to take over enemy units. Space RTS have it too. Star Trek Armada II has it, but of course, in star trek you have transporters. So if you manage to knock out the shields on enemy ships or installations, you can start transporting your crew to the enemy ship/installation. They even had special ships which were meant for this purpose, with lots of crew on board, and a special attack button (fire till shields down, then transport troops), and a special roam-and-board-whoever-you-come-across button.
Homeworld II also had special ships for this purpose. One side had marine frigates, which would fly up to the enemy, attach to the hull, cut a hole in the hull, and board the vessel. If not removed/destroyed on time, the enemy ship would be yours. I think the other side had ships which would launch small pods with troops, or something like that.
If you say 'yes but GC2 is not an RTS' then of course, you are right. But turn-based strategy games have the possibility of taking over enemy units as well. The diplomat or spy unit (which was it?) can bribe other units to fight on your side in the Civilization games.
Why not create a transfer module, which would work in conjunction with troop modules? Then you could use troop transports to seize enemy ships. In fact, what could be possible is that you seize freighters on trade routes, and for example get the revenue for that route for X turns.
Taking over enemy ships could either be part of the fleet battle, or be a separate type of battle you can fight out in some way or other; in the latter case, there can either be a system where you only need a transport ship to take over enemy ships, or a system where you need a powerful fleet with a transport as one of the ships.
Actually, since there is a 'number of troops' or 'number of colonists' stat, you could add crew to every ship, in addition to hitpoints. During battle, some crew would get killed. If a ship's crew is then dead before it runs out of hitpoints, anyone could take it over. If noone does, it's just stranded in space until someone re-crews it. If a ship lost it's crew, but the fleet it's in wins the battle, it shouldn't be able to continue with the fleet, unless one of the other ships re-crews it. There should probably be a special module to do this (also to be used as a weapon, by sending troops to enemy ships to kill their crew quickly). Also, the number of crew on board should not restore by itself, like the hitpoints do, but a visit to a planet would be needed to restore them. That way, in a war, ships would either need to return once in a while to get fresh crew, or get a visit from a troop carrier with a transfer module. Or visit a starbase, which would hold lots of crew of course. The transfer module would be standard on each starbase, and they could accumulate crew over time, like planet growth (but probably faster). The rationale is that they probably receive regular supplies from home, might as well send new crew too then.
