I lived on a course that was built in stages - it was 27 hole complex with a 9 and an 18. The 9 built first and had two flags on every green, a la Desert Mountain Renegade.
The 18 was designed with non-returning nines, which I liked because it forced the nine-holers to play the nine-hole course and kept them off the 18.
The 18 hole course opened in two stages. The first nine holes that were built were 1, 5, 6, 7, 8, 9, 16, 17, and 18. They played as a "back nine" to the original course when it opened, although they were just conventional one-flag greens.
The hole which was to be the 5th was a par-three, and just happened to be the one in our backyard. We liked it being in that position. It was a good place to sneak off and grab some drinks.
The original plan called for holes 2-4 to be built on the other side of a road, routed in nice woodlands along a natural creek which would have allowed for a magnificent split-fairway par five among two other nice holes.
Holes #10-15 were also really interesting, mostly routed around a lake.
The first thing that happened was that somebody decided there was too much water on the right side of those holes, so they flipped all of them to play in the opposite direction. The resulting holes were not nearly as interesting as those originally planned, and the longest par-five now played against the wind, instead of downwind.
Then something worse happened - the developer killed the three holes in the trees, and decided to have three new holes built completely on the other end of the property instead (boring, treeless farmland), so he could cram more housing lots. So the front nine became 1,5,6,7,8,9,10,11,12 and the back nine became 13, new hole, new hole, new hole, 14-18. The three new holes were all flat, featureless holes in the most open portion of the entire property and had stunning views of cornfields, county highways, and power lines.
The 5th hole became the 2nd hole. I'm not a fan of par-3 second holes.... it always seems to slow play down, and this one indeed became a bottleneck. It also wasn't quite as much fun passing the house that close to the beginning of the round.
In addition, the farthest point from the clubhouse was now about 1/2 mile further out than previously, making it a nightmare for anybody caught out during a thunderstorm to get to shelter.
Over five years I watched this course go up, and the original routing never got built in it's intended form, which really disappointed a lot of people. Once I got to play the course a lot, I couldn't help but feel the disjointed nature of how it went up ended up hurting it in the end.
I suppose this isn't entirely on topic, as it is more a case of a developer ruining a routing before it's even built.