Don't get me wrong... Pacific Dunes is one of my very favorite places to play golf anywhere in the world, but after playing each one several times now, I think Prairie Dunes is a better golf course.
I think it has an equally good routing, equally good bunkering, a better set of greens (every pin is a good pin!), a better set of par 3's (believe it or not), and more interesting fariway contours. The par 5's are probably a push (I like #17 at Prairie as much as I like #18 at Pacific), but I think Prairie has more great par 4's (I'll take #1, 8, 9, 13 and 16 at Prairie over #2, 4, 7, 13 and 16 at Pacific).
The "weakness" of Prairie Dunes would probably be the fact that it is primarily a championship course, and therefore not necessarily playable by all classes of players (I'd imagine it would be a tough place to learn the game, but the same could be said for Pine Valley). In fact, the high stuff growing on the dunes is so thick right now that there is little chance of playing a shot from it (but that's more of a maintenance issue than an architecture issue for me).
I'd also say that day in and day out, the turf conditions and speed of the course are probably better at Pacific Dunes (though currently they are just about ideal at Prairie Dunes).
If I do a match play between the two, it goes:
1. Prairie; Prairie 1 up
2. Prairie; Prairie 2 up
3. Pacific; Prairie 1 up
4. Pacific; AS
5. Pacific; Pacific 1 up
6. Prairie; AS
7. Pacific; Pacific 1 up
8. Prairie; AS
9. Prairie; Prairie 1 up
10. Prairie; Prairie 2 up
11. Pacific; Prairie 1 up
12. Prairie; Prairie 2 up
13. Pacific (barely); Prairie 1 up
14. Pacific; AS
15. Prairie; Prairie 1 up
16. Prairie (barely); Prairie 2 up
17. Prairie; Prairie 3 up
18. Pacific; Prairie 2 up
Again, it's very close between the two for me but right now I give Prairie Dunes the edge (although I'd probably jump at the chance to go to Bandon, Oregon again before I'd jump at the chance to go back to Hutchinson, Kansas...).
Of course, the next time I play Pacific I'll probably see something new there that tips the balance in its favor, but for now I'll go with Prairie...
Thoughts from those who have played both?