You would be better of staying on Phi Phi then as yes it does take aprox 3 hours to reach the Phi Phi area. A ferry will take about 1.5 hours to get out there and speed boat about 45 min. If you are looking for multiple days of diving then staying on PHI PHI is your best option if you can't stand the long boat rides out.
Some shops offer day trips from Phuket to just King Cruiser Wreck, Anemone Reef (or Shark Point), and Koh Doc Mai which is located closer to Phuket. This takes about 2 hours fro Phuket.
You can look for a shop- The Adventure Club and ask for an Instructor by the name of Timos who would take very good care of you.
Both Koh Bida Nok and Koh Bida Nai located just south of Phi Phi offer some great dives with abundant marine life, and can also be a good place if your wife likes snorkeling. You also have Shark Point the most popular site around Phuket, Anemone Reef, and King Cruiser Wreck a bit further out these would not be ideal for snorkeling on the other hand as there can be strong currents on these areas, and king cruiser wreck starts at 18m and extends down to 28m.
You also have Phi Phi Ley where you have a good chance to see black tip reef sharks and turtles the most.
Racha Noi and Racha Yai still offer some great diving so should not be over looked.
To see the bigger stuff then the Similan is your best option but it is a long drive up to the pier and then a speed boat trip out to the main boat for two dives. You could also consider staying in Khoa Lak and take day trips out by speed boat and still have some great diving. For this I would recommend Khao Lak Scuba Adventures. This year there have already been a lot of sightings for the larger marine life.