I have not been there in the last 12 months. Friends have. It was not their first trip there. However, I have been there twice and have also been on the Pelagian, none recent. I also know some people who on the Pelagian within the last two years. Here's my opinion and it includes the hearsay from others I know.
In a 5 star rating system, I would rate the diving at Wakatobi a 4. It is quite diverse with excellent macro, walls, corals, and fish life. It is not on par with Raja or Komodo, which I consider 5 star. There are other 5 star diving places, but they are generally a narrower focus, e.g. macro or big animals.
Room, food, and comfort are 5 star. Diving is a bit regimented, but efficient. It is well run, despite a constant churning of staff. You will have a great time. You will not be unhappy, especially if you haven't done Indonesia diving. (I've done 13 trips). The food and food choices are outstanding. The rooms are as roomy as you could possibly need. The amenities are plenty good enough.
The Pelagian is luxurious, but we didn't like the boat. Four great rooms and one crappy room. Nice inside lounging, but little outside lounging area. The diving away from the resort wasn't as good as the resort. I would give it a 3. The only advantage is that it holds a max of ten divers. While your dive boat at Wakatobi may have only 12 divers, the resort may have 50+ guests.
Two biggest complaints are about the pricing and there are plenty of Lorenz haters: While prices have gone up dramatically (we paid $2880 for 10 days which included the charter flight), it is not crazy compared to a top notch Raja liveaboard, which can run $500pp per day or even more. As for Lorenz, the nominal owner, once you get to know him, he's not very likable. No worries, you probably won't get to know him or even meet him.
Recent reports indicate no major changes with my old views. I'd rather book the resort than the Pelagian. There are those out there that feel the opposite. BTW, the house reef is among my personal ten best dives sites I've experienced and plan to write about, but you must do it several times. That's my take, good and bad, but just remember, regardless of whether it's the greatest diving in Indonesia (it's not), you will greatly enjoy the diving and the resort.