Hotel in Victoria
Two years ago, we stayed at a wonderful bed & breakfast called the Prior House. We had a small room, but had a look at one of the palatial suites (!). The breakfasts were fabulous, and the hosts were very helpful with restaurant recommendations. Parking is free; it's about a 5-minute drive from the central waterfront area. See the link below.
Near Victoria is the Sooke Harbour House in Sooke. They also have a website at www.sookeharbourhouse.com We had a nice dinner there one night, but it is very pricey. I think the rooms look lovely. One of the other couples at our B&B summed up S.H.H. as "Fussy, hoo-haw, overpriced, right?" We agreed, as far as the restaurant was concerned, although it does regularly appear on lists of the 'best' restaurants in Canada. Our best meal in Victoria was at Brio, which was recommended by the B&B folks. If you see any wine on a list from Blue Mountain Vineyards, order it.
I'd suggest getting in touch with one of the local realtors - There are beautiful condos right as you enter the harbor that I believe are rented out on a weekly basis. They are literally right on the inlet and the view of the ships coming and going is terrific.
This group of condos is right next to one of the most beautiful hotels that is on the opposite side of the harbor from the Empress Hotel.
Victoria is beautiful and well worth going to for your honeymoon - Congrats.
In downtown Victoria, the best hotel for the money is a boutique property called the Magnolia. Approx. 80 rooms, great service and location.
However, I would recommend spending at least on night at Hartman House B&B in Sooke. You are close enough to go to the Sooke Harbour House for dinner (which is not to be missed) and yet do not have to pay the big bucks for the small rooms. At Hartman House ask for the luxury suite. It has a four post, hand carved king size bed and a jacuzzi for two with a fireplace. Breakfast is left in a private corridor and then can be wheeled into your suite at your leisure. And the breakfast is to die for :)
If you call, tell Anne I sent you.
In Victoria, do not miss Cafe Brio as someone else mentioned, but also be sure to try Camille's for an intimate night. It is so good that my wife and I drove over on the night of our wedding from Vancouver and made it our first stop.
Have a great trip!