Just returned from a couple a weeks of diving in Truk and Pulau. Trip was great, thanks to my local dive shop.
Truk: stayed at Blue Lagoon and used Blue Lagoon Dive Shop
hard to pick a "favorite", depends on what you are looking for. The ships are so large, and there is so much to see and absorb, you could spend a week on each one and not see the same thing twice...
1. Shinkoku
2. Fujikawa
3. San Francisco
BLDS does an incredible job of showing people the wreck highlights and letting you discover stuff on your own. This is more technically oriented diving and having previous deep/wreck experience will be a big plus. The BLR accommodations are "rustic" but adequate and the service was very good. The lack of sharks in Truk was disappointing, too many have made their way into the soup pot. :depressed:
You're just not going to see that many sharks inside an atoll lagoon.
To the OP, here's a link to my trip report there seven years ago. The wrecks have not changed significantly: http://www.scubaboard.com/forums/pacific-islands/28819-truk-report.html