When I started working on my vision for a DC Cinematic Universe, I had way more than just three Batman films (I had five in total). However, in a revised version (which I can consider the final version eventually), I have three of the best stories that I would base a trilogy around.
Batman: Knightfall as the first movie.
Batman: Hush as the second movie.
Batman: Under the Red Hood as the third movie.
That's what I would do.