We stayed at the Crowne Plaza (Melbourne) in December and we loved it. We got a 2 room queen suite with ocean view for 126.00 a night. Not bad, and because they were willing to work with us and Doubletree wasnt, we went with them. But as others have said, there are only 4 in Melbourne, but all 4 look equally as nice. It's all personal choice when it comes down to it, and price of course.
Cocoa Beach has a lot of activity near by the hotels, but your 2 yr. old will like either. The one thing I like about CB is the restaurants around the Port, and of course watching the Cruise ships go out. You might even enjoy Ron Jons or Cocoa Beach Surf Company like we did.
We used to live in Melbourne, (26 yrs.) and things have changed in both locations. You will enjoy both, and depending on whether you are coming over to the coast on SR 528 or 192, one will be more convienent than the other.