I use a PS2 Controller thats analog stick is physically missing pieces.

Fits me like a glove and has given not too many issues. D-Pad was never good, it was required and thats arguably the best answer in regards to that. Some controllers will physically age though so a PS3 controller if you are used to it would be entirely better. It's pretty much Comfort is King

I mostly feel more comfortable with the PS4 controller when I was doing emulator runs. Even with the PS1 controller I now have for Silent Hill speedrunning, I'd still prefer the PS4 controller. I guess it's what you're preferable with.

Just make sure that the controller has an analog stick, so you don't lose time on cursor movement. Otherwise it is personal preference. I have played this game on a DS1, 2, 3, and 4. I prefer 1 and 2 mainly due to the shoulder buttons. 4's Dpad is less hard on my thumb in my experience.

In my first 10-15 attempts in speedrunning Silent Hill, I kept getting hit from the monster inside the cafe, because of the PS3's trigger button, that is totally unsuitable as an "R2". But I don't dare to change that button, I already have too many things to remember about this game. PS4's D-pad is of very high quaity, no doubt.