If it supports a controller, I'd definitely prefer to play with one. I can also adjust to a comfy position and lean back in my chair. Sitting up straight for too long is a sure way to mess up my lower back
I use a controller for playing vns because I also play a lot of rpgs, particularly jrpgs, so it's just more convenient and comfortable for me. The only time I don't use it is if the game doesn't support it.
There are times when I use a gamepad. It is convenient when there are many buttons needed. However, my gamepad makes a loud noise when I press the buttons. Therefore, when I want to read VNs quietly, I end up using a mouse.
