Indeed, all my .pdf files are set that way. However, when I import the same files into iBooks they revert to opening with Preview. This began after the latest update. Apple wouldn't force me to use Preview, now would they?
Based on the complaints against the simplification of Pages (to make it compatible with the web version) and no fixes, it might be that iBooks will always use Preview going froward. You need to either find a replacement or an older copy of iBooks (like from a backup).