I just got another idea today.  In First Contact, the Borg transport to a strategic location (engineering) and preoceeded to try to take over the ship.  What if the other races could choose where to transport when transporting an assault team?  You could choose to transport to enginering, the bridge, etc.  Places would have advantages and disadvantages.  Say, if you transport to teh bridge, you could only transport five people, but you take over the whole ship.  If you transport to a torpedo bay, you could take over the weapons....

Also, the crew of the ship would not be killed, but insted captured and used against the enemy.

Nice idea but I think without the 'bridge' one, why damage a ship's weapons or engines when you can just take the whole ship? Would be too easy.

What if an 'extreme' assault ship was made, one that transported it's whole crew to a station, immediately taking it, it would be expensive and be lost afterwards but could be worth it in certain situations