Why not make the transporter a skill we can add to our skills for all classes? it could work like this...lets say for starters you orbit the place you want to beam to and you see the "ground map" of the area you will beam too? Then from your ships interior instead of external view, you go to transporter room to call it up.
As a start of the skill you have the choice to beam "x number of enemies" to either space to kill them to make mission easier, or to brig to "interrogate" for upcoming mission info like remaining guards, or "where are the bombs placed?", etc.
Also the skill would have another advantage. During a ground mission you can swap unconscious boffs to sick bay for other boffs on a pop up list or security boffs till sick bay heals them to send them back to you. Also you can beam down replicated supplies as i listed in my "trekienomics" post
Basically the skill can be leveled up...without a cool down or recharge time because the ship has numerous transporter rooms anyway. It will beam out enemies, allow you to choose custom boff/player beam in points as a group or individual locations...sniping setups etc. You can also beam in supplies and beam out unconscious players to swap for temp boffs till default ones are healed and returned
So lets say you are a lt. you can beam out 2 enemies and replace one boff and beam in 5 supplies as well as one beam in spot. Raise it one notch and its say 3 enemies out replace 2 boffs and 6 supplies beamed in and 2 beam in spots for you and all of your boffs. 3rd notch is 4 enemies,3 boff swaps at a time and 7 supplies and 3 beam in spots (one for you a spot for one boff and the rest in the final free spot ).
Once you have all 9 marks leveled in rank skill is maxed out for the game but with a really good top out point...say... 75% enemy beam out map wide, custom beam in for each boff and captain, unlimited supply beam ins and all boff swap for healing and returns.
Also if the player/captain is unconscious the skill can beam him to ships sick bay while he has a "security team" of up to say 4 boffs beam in to take his place and he remotely directs his mission from the transporter screen while lying in bed getting healed. so it can work like a mini RTS game until he/she is healed...by say get 4 kills in transport screen commands and you are healed then player can either choose to beam in at any time like earlier or finish the mission from an "OPS Station" perspective while the ship is in orbit.
That only happens if captain was shot unconscious and beamed back to ship. However captain can swap crew members in and out of map manually as he sees boff stats drop like in the ground mission while player is healing or continuing to direct mission from ops Station on bridge.
If teaming with another player the wounded player can beam to their ship and use their transporter room to assist the other player. If both Captains are out then they both "run the mission" via their transporter rooms/OPS Stations assisting their boffs like an RTS game...remember Picard wasn't "allowed" on away team missions anyway right? This is an "option" for that view.