Player agency is defined by a player's control over the way a game plays out. It is so much more than controlling units or issuing orders. Here are some examples of player agency:
1) cities skylines: player agency is expressed in the actual design of the city and how the city grows and appears over time is the unique result of player expression. That kind of uniqueness, and the way the city plays out, is tailored to the player and a unique result.
2) minecraft: Yes, I hate minecraft comparisons also, but I'm going to do it anyways. Player agency is expressed by the architectural and artistic expressions of the player by mining and placing blocks, redstone creations, player housing, etc. It's indisputable that everyone's world is so unique and plays out the expressions of the player with nearly every action.
3) dominions 4: A lesser-known title, but a great example of designing an RTS that has such incredible customization and ways to affect the world that there is uniqueness and control as to the way the war plays out every time, such as customizing the attributes of your civilization.
So now that I have given three examples, I want to talk about very simple ways that you can have the game play out uniquely under the control of the player.
1) Turret placement. This is an easy one. The player is able to create designs and strategies that are a direct reflection of the players' expression. In recent years, this has been optimized by the player and could use a refresh, but that's a different discussion. I just wanted to show a positive example of player agency that we already do now in AI war classic.
2) Smoke and debris. These are dynamically generated based on actual unique battles, so the way a battle looks and the aftermath reflects the unique expression of the player.
3) Ship customization, base customization.
