Your great course challenge, what about Machrihanish? I have no idea of a better routing could be had, but I always feel the back nine seriously peters out causing a flow issue for me. Its not good enough that there ar X amount of good holes when talking about the best courses. The spacing and flow is also important and this is where I find Machrihanish sorely lacking when I compare it to a course like Pennard with its cool holes spread wonderfully through the round.
Sean:
I do agree with you more than I've been saying. In the past ten years, I've decided I'd rather put the tee for a hole closer to the previous green, instead of at a better vantage point ... actually the 6th hole at Ballyneal was my "aha" moment there. But I wouldn't have done so if I'd thought it really made the 6th a substantially worse hole; I just decided the "perfect" view from the tee didn't make as much difference as some others think it does. The blind tee shot there actually gives the course more variety.
As to your example, I agree that Machrihanish would be a better course if they had mixed up the holes better so that some of the best ground was on the back nine rather than the front ... as long as they still came up with the same number of great holes that way. I don't know if that would have been possible or not ... although it seems that the present 1st tee was once the site of the 18th green [perhaps a crossover, with the 1st tee in tighter to the clubhouse], and they went away from that. But, you don't think it would be a better course if they just built the clubhouse up at the other end, so the back nine was the front, do you?
Likewise, to Archie's example, Royal County Down is often knocked because those last three holes aren't as good as the rest. It IS a disappointing finish, and they keep messing with it to try and fix that, but all those bunkers on the 18th didn't help a bit ... they'd need to be a lot more clever to make that ground into something compelling. But, again, would the course really be any better if you took the same 18 holes, and just put the clubhouse out by #6 green? It wouldn't make much difference to my opinion of the course.