Generally, the first ship of any class suffers the most issues. Similar to the first version of any major OS/software release. I don't remember the per-ship costs off-hand but I'd be surprised if they were higher than the first.
Unfortunately the Navy doesn't have much choice in who builds their ships. They must be built in the US, and there are very few capable shipbuilders still left in this country. It's a terrible business to be in, so there's no incentive for companies to jump into the market because the margins are razor-thin. In fact, Northrop Grumman got out of the market a few years ago (http://investor.northropgrumman.com/news-releases/news-relea...).
(As an aside, cruise ships are still cookie-cutter compared to military ships.)
To borrow a quote from Churchill, "[the current ship procurement process] is the worst form of [procurement], except for all those others that have been tried."