My personal favorite for most games is a regular TG16 pad. The Ave 3 would win out but the buttons don't feel quite as nice to me, I'm not sure if it's just my pad (it was used, probably worn) or if they are all like that, but the buttons seem to rub a little, like the hole is a hair too small. I've entertained the though of trying to sand or drill it a hair larger, but I haven't had the stones to try it out yet. Other than the button thing, the third button comes in handy in so many games it's ridiculous. Dracula X, Super Star Soldier, After Burner 2, Shinobi all make great use of the third button without technically being 3 button games.
I like the Ave 6 more than most people, but I rarely use it for anything but 6 button games since I just prefer the other pads for 2 button games. If it were the only pad I had it would be fine though.
I shouldn't technically include this, but the BEST controller I have for the thing? A Saturn pad. I built a converter box a while back using a Cthulhu board that converts the Saturn pad into damn near everything, including the PC Engine. 9 times out of 10 though I'm too lazy to drag the converter box out and just use a regular PCE pad.