Our major complaint is the internet connections. We did not have a cell phone for international use and so, we had to rely on the internet to be in contact with our family. At 65 cents per minute, this is pretty expensive; it also applies to wifi access. They offer a package, but we had so many problems connecting to their internet, it was just too expensive! Everyone was complaining about this; the staff at the front desk was very nice, apologizing, crediting your account, etc., but this is no way to solve the problem. We wasted more time, just trying to access the internet, only to be frustrated, etc.
Another problem, as many have stated, is the tours that the ship sponsors. We had a full day in Jerusalem; due to horrendous traffic (and we believe poor planning on the tour company's part), we wasted hours in terrible backups. We barely had time to go to the wall in Jerusalem; instead, our last stop was at some "diamond" (and very expensive souvenirs) store. We were there for close to an hour (when time would have been well spent in the Cotel). We would definitely recommend either hiring a private driver or just taking a cab to/from the ship into Jerusalem.
As mentioned, it was a great trip and we definitely recommend it; just be aware of these few items.