Please don't completely give up on ship combat! XCOM:EU has both real-time effects and ship combat, and it functions acceptably without adding complexity or confusion. As long as ship combat doesn't have a fail-state (ie: losing combat forces a game over), then having (essentially) minigames to increase play agency and reward (ie: fewer enemies or better strategic entry points).
I like the idea of having the tactical choice of how to damage a ship in order to better breach it or salvage choice selections.