As you've already heard, beaches are hard to find in the Keys given the Keys are essentially coral islands. Key West has a decent beach on the south or ocean side of the key (can't recall the beach's name) and Fort Taylor has a decent beach, but it is a little rocky; bring aqua-socks. Bahia Honda has a decent beach. None of these are anything remotely like Miami Beach or Sarasota. If your wife really wants decent beaches, you can stop off in Jupiter or elsewhere in Palm Bech County, Broward County or Dade County for a day or two before or after hitting the Keys. The diving in this part of Florida is also good (in some ways better if you want to see sharks, goliath grouper and other big critters) and beaches superior.
All the deep wrecks in the keys are worth diving: I've been on the Spiegle Grove, Duane, Eagle and Vandenberg numerous times and always found something new or interesting on each dive. Aside from the attraction of the Vandenberg, I like diving in Key Largo and Islamorada better than the rest of the Keys.
Reefs I like include Hen's & Chickens (most unique reef I've seen in the Keys), French, Davis, Snapper, Molasses, Conch Wall (one of the few deep reefs). Actually aside from Spanky's, all the shallow reefs are pretty nice. Oh yeah, just to say you've done it, dive Christ of the Abyss.
I dive with Conch Republic most of the time. I've also dove and enjoyed Rainbow reef (provides guides), Quiecence (six pack) and Silent World (will let you dive to your certification level on deep dives).
In the Marathon area I've used Dive Duck Key and in Key West I've used Captain's Key.