Earlier this year we did a week on the Palau Aggressor, and followed it with a week at the Manta Ray Bay Hotel. As great as the diving was on the Aggressor, oddly, we wished we'd spent both weeks on Yap!
The Manta Ray Bay Hotel is superb. There's no other way to describe it. Our flight arrived in the middle of the night, and the hotel manager was there to greet us by name. Wow. We had our room number before our bus left the airport - check in was "here's your key"...and it just got better. The rooms were clean, in fantastic condition, impeccably maintained and air conditioned. As good as the hotel is run, the dive operation is even better. Clean, in fantastic condition (just ask to see the compressor room!) superbly organized. And, they let you dive "your way", and made the boat schedule fit what we wanted. Everywhere you look, it's quality.
The building and grounds are impeccable. The bar is on the top deck of an old sailing ship, in the breeze and above the bugs.
It would not be an understatement to say that the Manta Ray Bay Hotel is the best shore op we've ever seen - and we go to 2 or 3 a year.
Yes, the wrecks of Truk are spectacular, and are deteriorating, so you should see them now while you can. However, given the worn feel of the shore operations (almost borderline adventure diving in some cases), I would not return unless I was on board the Odyssey liveaboard. Much can be inferred from the 1 year waitlist to get on that boat, as opposed to the wide-open shore availability.
Go to Yap. Taken as a whole, it is an amazing diving experience. Go to Truk after a considered preparation, both in the liveaboard, and, in classes such as deco, that will give you better access to the wrecks so you can really appreciate them.
All the best, James
PS-given the airline scheduling, I would do Yap after Palau. Otherwise you'll have some very late nights for your flights.