I was playing through the mission "Everything Old is New" from the Devidians featured series when you travel through the time portal and arrive on Drozana Station in the 23rd Century and after one of my away team officers suggested that we set our weapons to heavy stun, I asked myself, why don't we have the option to set our space and ground weapons to either stun and kill which is completely Star Trek. Now we have all played through missions we find in any star cluster where we have to defend a friendly base on an asteroid under attack, beam down to an asteroid base that has not been in contact with Starfleet and find out why, clear out an area of space with hostile ships, and free a planet that has been taken over by an enemy force. So I started thinking about the concept a bit more and here is what I came up with.
For example, you enter a star system where an otherwise peaceful planet has been taken over by force by hostile baddies. All you have to do is hear that the planet is under attack, move into relative orbit above the planet, and receive the message from the baddy leader ordering you to leave, beam down to said planet, defeat all the baddies, and beam out.
Now what I propose is this, you enter the star system, get the message from the planet for help and encounter a ship from the enemy force currently on the planet and you have a choice: either set your ships weapons to kill and destroy the ship completely OR set your ships weapons to disable the enemy ship, you then beam over to the enemy ship where you must make a second choice: kill the enemy crew OR stun them where they are then transported to your ship's brig. Now to take the enemy ship, you must reach main engineering and/or the ship's bridge to complete whatever assigned objectives which may include killing or taking the captain prisoner.
Now once you have taken the ship whether you did so through lethal or non-lethal force, you beam back to your ship and proceed to the planet. You then receive a message from the leader of the hostile force on the planet who tells you to leave the system as the planet belongs to him/her. And now you have a third choice: if your diplomacy rank is high enough, you can "persuade" the enemy leader and his forces to surrender and if you succeed, this mission is a success and you receive diplomacy points. But if your diplomacy isn't high enough, you will deal with the enemy force the old fashioned way. You beam down again setting your weapons to stun or kill. You kill the enemy and beam out OR you stun the hostiles and beam them to your ship's brig as prisoners and once the planet is free, you beam off the planet and leave the system BUT the prisoners remain in your ship's brig until you reach the nearest starbase and to make this interesting, the more prisoners in your brig, the higher the chance of a prisoner escape on your ship which you as captain must deal with by returning all escaped prisoner to the brig. As for the weapon stun and kill setting as well as boarding a disabled enemy ship, which could be applied to any star cluster mission.
OK, if my suggestion isn't long enough already, let me add the icing to the cake. I've just made though I realize the very low likely hood of ever seeing something like this happen in game but here goes: After you have taken so many enemy prisoners, there is a 2.5% chance (2.5% being based on all weapon procs and is good enough for this idea) that one of these prisoners will admit what he/she has done is/was wrong, want to change his/her past evil ways, and request to join your crew which you can either accept or deny, the choice is yours Captain. And/Or after capturing so many enemy ships, you will be contacted by Starfleet and told that this enemy ship which you disabled is too damaged to be of use by Starfleet and is given to you to be done with as you see fit. Now to your choices: 1. you can sell the ship via a DOFF mission and take the Blue/Rare rewards OR you can have your crew strip all usable equipment and sell the ship for more but Green/Uncommon rewards. 2. You can keep the ship and have your crew repair the ship to where it is returned to space faring condition BUT to accomplish this, you must complete several DOFF missions (with longer than normal timers) that may or may not require resources (Energy Credits, Dilithium, Data Samples, or possibly even Gold-Pressed Latinum) to complete. And once complete, you now then have a brand new, clearly second hand used, and completely repaired until you venture it into battle and take the usual damage that will be repaired by you and your crew starship to your own personal stock.
What do you think and please remember that all ideas in this game expanding suggestion are subject to change or improvement.