Which emulator were you using, because I've seen YouTube videos where it it looked significantly better than the original version on PS3.I recently tried to emulate it, using a controller to keyboard adapter. And technically it ran. But it's such an annoying experience. The input adapter isn't good really, but I guess you can get used to that. But then you have to find workarounds for locking your cursor to the context of the emulation window, so that you can control character orientation, but not also operate whatever you have on your pc's desktop. And it also runs kind of iffy, even on my hardware. Doesn't really look very good. Even worse than I remember it on console. You really have to want to play it, to endure all of that.
As for the input, when you try to play something using a control scheme that it wasn't meant for, it's rarely going to feel natural.