I agree with MR. Think of it this way, if you want to make it more ‘lethal’ for ship combat, have them face 2 ships one to two scale below them in an area or situation where they can not simply jump to warp. For example, when tasked with defending civilian cargo ships.
Using the following ship as the player ship for the following example: https://drive.google.com/open?id=1r3h3TUgw6Vb77dur_ZL2k1JoGyY-Hhox
Enemies for this scenario: 2 Jem’Hadar Attack Ships. (p 264/265 of core book)
If there are 4 players, you should have at minimum 8 threat (possibly more if this is not at the start of the mission). Spend 1 threat to have the Jem’Hadar go first, signifying a well-executed ambush, and have one ship enter an attack maneuver, spend 2 more threat to keep the initiative. Have the second Attack Ship fire a Phased Polaron Beam at them, targeting their weapons (spend 1 threat to purchase additional D20 for attack.)
I just rolled this out, 4 dice for the attack (2 for the crew firing, 1 for ship, 1 purchased) with a difficulty of 3 at medium range. Oddly enough, I rolled a 5, 6, and 7 for the crew, and a 5 for the ship. That is 4 successes which would give you one threat back and hits the weapons system of the ship dealing 8 CD of damage to the weapons. Rolling those dice, I got 3 effects, a 2, 1, 1, with 2 blank. Spend the threat you just earned to reroll the two blanks, get a 1 and another blank. That’s 8 damage with 3 effects of Piercing 2 to the weapons system. I believe that negates their resistance, which causes a breach to the weapons and drops their shields down to 9 (4 without Advanced Shields). That is just the opening volley, so to speak. Both Attack ships still have 4 more actions in the turn, and the ship that hasn’t fired yet is setting up for an attack against the ship, which will most likely be a close range Disruptor Cannon strafing run.
If you had 3 Jem’Hadar ships instead of 2, you could have 2 attack from medium range from different sides, while the third made the strafing run, with all of them aiming for the weapons first, then engines. If all else failed, one ship would make a suicide run at the player ship. It was a common tactic of Jem’Hadar.