Since this is your first post, I hope that you have not come to this forum only to complain and will be participating in the many posts you can contribute to.
In the meantime, welcome to Cruise Mates and we hope you'll stay for a while.
First and foremost; this is one of the best reasons why you should always book with an agent and never directly with the cruise line! If you book directly with the cruise line and you have problems, who do you think they represent; you or them? An agent represents you and they have your best interest in mind, so they will work hard to insure you're taken care of.
Also, I would almost never suggest booking airfare or transfers through the cruise line. It's almost always much better, cheaper, and easier to do these independently.
As for some of the things you addressed on the ship, unfortunately alot of these things are uncontrollable nor unforeseeable. But I definitely understand your frustrations. It's not usual for repositioning cruises to have some repair work going on during the cruise. They'll often bring on contractors to do the work while spending many days at sea. However, they should have informed passengers ahead of time so you decide whether or not you wanted to make the cruise.
Your agent would have made sure that both of you had your Gold Membership applied to your reservation, but for RCCL to say you qualified for priority check-in and not your wife is inexcusable! As long as one person in the stateroom qualifies, everyone in the stateroom qualifies.
I'm sorry your experience was not up to what you have come to expect from Royal Caribbean. Hopefully, your future cruises will meet your expectations.