Rory,
I think the routing at French Creek does suffer from the constraints of housing and wetlands. There are several holes with large distances between tees and greens (3 to 4, 8 to 9, 13 to 14, 15 to 16). As you point out, Hanse is very clever with the architecture out there, and the course maintains a good flow throughout the round. However, the site makes the course very difficult to walk, and I found Inniscrone a much easier walk throughout the round. The routing at French Creek may not make a difference to most people, but it does make a difference, albeit minor, to me.
The comparison between Inniscrone and French Creek is tough in a different way. The styles of the two courses are dramatically different, especially considering they were built by the same architect. French Creek uses large, bold bunkering and some wild greens, whereas Inniscrone is much more understated, with small greens that tend to have one dominant contour and bunkers that are used sparingly. There is a lot to love about both courses, and, in the end, I would place the two right next to each other in terms of quality. Inniscrone's bad holes are worse, no doubt about that. Inniscrone makes up for it with some standout holes and a rugged boldness that I wish I saw in more layouts.