I actually prefer the middle of the course to be the strongest part of the course. I look at courses as having at least 3 but more often four sections. Start, front middle, back middle and finish. The intro is important to set a tone and warm you up to the challenges ahead, but these as a whole don't need to be the best holes. The middle is where the battle lines are drawn and ebb and flow to these holes is important. The finish doesn't need to be the best as many matches are already decided before the final holes, but should require quality golf to close out a match.
Crystal Downs is a great example featuring a strong start with 1 great hole and 3 others that introduce the character of the course, 5-9 being world class superb, 11-15 also superb but with a different characater, and 16-18 finsihing the round or match with holes that may not be as good as the rest (17 is a bit too quirky for a finishing hole imho) , but still requiring quite good play to finish off a match.
At my favorite Lawsonia, I also see 4 distinct segments. 1-4 ( a good start with two very strong holes (2 and 4), 5-8 (great character to 5,7, and 8 with 7 the best hole on the course) , 9-13 (the funky 5-3-5-3-5-3 segment of the course), and 14-18 requiring very strong play at the end of the match while lacking the charm of the middle sections.
So I don't think it really matters which nine is better, but the finish (last 3-5 holes), while not needing to be the best part of the course, shouldn't be weak.