I'm in a middle of drum tracking session for an album, and I can tell already that I will keep the toms 100% natural, maybe even the kick! The drummer has feet consistent as fuck (never recorded anyone like him, every kick hit even in double bass parts comes hard and with same velocity) and great sounding kit. The only thing I may have to reinforce with samples is the snare, for two reasons. His hits aren't always as hard as they could be, and the snare isn't very deep so we had to tune it really high to make it come alive, so I'll probably add meat with some other sample. I wont replace it totally, of course.
As it has been said, coming up with great natural drum sound comes from a lot of factors, and if even one of those fails you're pretty much fucked up. Great drummer, great kit in tune with new heads, good room, miced properly.
The tuning of the snare has been bit of a pain in the ass also, first two recording days the tune kept going flat and I had to bring it back up a lot. Luckily I had Tune-Bot! That thing may be one of the best purchases I have done related to audio. After tuning the toms with that.. Sweet. The look on the drummers face was priceless.