You are in for such a treat in Australia! To answer your questions... we were there from May 24-June 11 last year and the weather was absolutely fabulous. The typical temperature was between 75-80 F unless you were in the mountains and then it could get down right cold (I'd guess around 40 at night and 60 in the day). The water temp was 80 F and we chose to wear full wet suits. I am always cold do I chose a 3/5/3 mm and my husband had a 3mm. Others on the boat wore shorties and they were 3 mm. Just depends on how long you're down and your tolerence level. We did not experience any thermocline and our deapest dive was about 100'. Visability was at least a 100' on every dive and it never rained. We took a sea sickness pill we got from CVS. I can't remember the name but it was chewable and had an orange flavor. I also used sea bands which I swear by (they are the elastic bands you wear around your wrist). I use them in the car all the time because I have a terrible time with car sickness. They work for me! Anyway, I never got sea sick and after the second day, I had stopped taking the meds. The water was really calm because we were inside the reef.
As far as the land stuff, we had a car and drove up into the Atherton Tablelands and up north along the Bloomfield track. Different climate and wildlife everywhere (just make sure you move slowly and quitely and you will see the most amazing animals). We looked around the towns and stayed the rainforest a couple of nights. Took lots of walks and we did a couple of tours with naturalists (Wait-a-while Tours and David Armbrust). We also did something sort of "touristy" but we loved it... we went to the Rainforest Habitat for their Breakfast with the birds. The Habitat is just outside Port Douglas and it was a great opportunity to see the birds we we heard in the wild and identify them. The Habitat also has an area with Kangaroos and crocs and all sorts of other critters. We also rented a plane, flew out over the reef and then flew inland to Undara to see the lava tubes and the edge of the outback. We thought it was spectacular out there. Maybe not for everyone but it was so different than the coast, reef and rainforest. We spent a day and a half there and both of us agreed that we would have liked to have spent more time there. We also spent a couple of days in Sydney. We aren't "city people" but we really enjoyed our time there as well. Beautiful town with lots to do. Very clean as well. There were so many other places we would have loved to have seen but we'll have to just go back. The country is just so big that we decided to just concentrate in one area. I think that was the best choice because I think you'd miss a lot if you tried to see everything in 2-3 weeks.
Anyway, have fun!