I have played both Pac Dunes and Ballyneal. In my personal rankings I actually have them 1 and 2, respectively, so you can tell I love both courses. I was thinking while reading this thread why I have them in this order and what I came up with partly is in regard to the par 4's.
At BN holes 2, 6, 10, 17, and 18 can all play very long depending on the wind. They tend to beat you up a bit and can be hard to get to in regulation with a strong enough wind. At Pac Dunes there aren't really any long par 4's that I feel beat you up and I think overall this makes the course a bit more playable. As mentioned in an earlier post maybe #7 and #13 into the wind, but I don't find those holes overly long. Overall Pac Dunes, even from the back tees, isn't a long course and with the winds blowing hard I feel that you can still get at every hole out there and that makes it a lot of fun in all conditions.
On the flip side, however, the longer par 4's could be seen as a positive at BN because with holes 2, 17, and 18 running roughly the same direction and 6 and 10 running the other way you are pretty much guaranteed to get at least a couple of long par 4's at some point during the round making the course more challenging. Likewise this would mean that the other two or three longer par 4 holes would be downwind. I did find BN the more difficult of the two courses.
It's a tough call, but also throw in the Pacific Ocean and I've got to give the nod to PD.