John,
I cannot comment on the Village, plus it is a NLE (I think...isn't Faz. doing a renovation?), but I have played the other two.
The Bay course was a basic resort course, IMO, with the exception of a couple really great ocean holes. It winds its way through cool Hawaiin trees, going up and down across some pretty hilly terrain. Overall there is indeed some variety, but not every hole is a good or great hole, and except for the ocean holes, there are none that really jump out as being spectacular.
The greens were fun, and as it was my first experience on Bermuda-grass, they proved, for me, very challenging. The contours were subtle and compared to the Plantation they were relatively (*edit*) flat , but they were playable and puttable for people of all ages and abilities, which is a good feature for a resort course.
The front nine winds its way through some houses before hitting the ocean on 4 and 5, and then goes back through some houses to the clubhouse. A couple of the holes got a bit sloppy, I thought, such as the short par-5, uphill 6th, but nonetheless the ocean holes made your mind drift otherwise.
The back nine is on the higher portion of the property and is relatively hilly. On almost every hole there is a view of the ocean, which is very nice. Overall the back trumps the front, IMO, design-wise, and funwise it has its little quirks too. For me, it is fun to see the ocean whil I am playing so the fact that most hole had a great view made my time really enjoyable. The 18th hole is a good closer, going down a little valley and then back up, to a green perched below the beautiful clubhouse.
My only real bad-talk of the Bay course is that their range balls were the weird kind with the dimples on the outside of the ball (maybe Cayman balls?). Since the wind was strong and I was not used to that, I was a little bummed I couldnt warm up with real balls to see how the wind affected them, but it was till OK. Golf is golf.
The Plantation is just fantastic.
The first hole has huge bunkers engraved into the hillside, with an elevated tee shot, and a huge fairway, which makes for a really inviting first tee shot. Then the green is benched so a longer approach shot can be banked onto the green from the left, and bound towards the green--and ocean. From the first hole on it only gets better.
I found that I really loved the greens, and how each one seemed to blend in perfectly with the hole. The greens all had crazy, but different contours. One thing I really liked about the green complexes was that most of them would except a running approach, or an aerial approach, which is good given the wind is so strong up where the course is.
The par fours offer a great variety, each representing a real challenge, while at the same time being very fun to play. If I recall there are two driveable par-4's, and one of them is about 365 yards! The cool thing is, even though the hole is very far downhill, great design is used. The green is divided by a huge ridge in the middle, seperating it into a big left tier and right tier. This is a good concept as a shot approached from atop the hill still has to be carefully judged, yet the person who finds his ball bounding 100-some yards down the hill is left with a tough chip/viscious putt. The other driveable par-4 is 100% different, as it is uphill with bunkers guarding a lay-up shot and a small green that requires precision.
Obviously, the closing holes are as good as about any closing holes, at least as far as how fun and dramatic they are. Each hole runs down a ski slope and though they are over 1100 yards together, they can each be reached in two, and sometimes with a shorter iron on #17. They provide to a fitting finish for a great course, IMO.
I will be playing Mauna Kea, Mauna Lani, Princeville, Poipu Bay, a Paukea next year so I will see if Kapalua is (at least IMO) the best course in Hawaii. Without playing any of the courses mentioned above, though, I can definitely say there would have to be something pretty special and amazing to trump the Plantation course.