Hi Christophe,
I own a dive resort in Kosrae, so I will "try" to give you unbiased advice on the diving here, based on what our customers tell us about their experiences in Micronesia. Of course I will give you more information about Kosrae than the other islands, as that's what I know best.
Palau - not to be missed for up close action with large pelagics, plenty of WW2 wrecks above and below the water, excellent macro if you can take your eyes off the big stuff. Up to 1.5 hour boat rides each way if you aren't on one of the many liveaboards.
Yap - Excellent chance of seeing Mantas, although as usual, the vis where they are is low.
Truk (Chuuk) - It's hard to beat it for wreck diving. Most of the dives are 80" ++, the guides will motivate you to penetrate, so best to be very comfortable in the water when you arrive there, maybe make it your 2nd stop if you won't have dived for a while.
Kosrae - Won't have large pelagics everywhere or Manta's, and very few wrecks. Will have, the healthiest hard coral you will have ever seen (anywhere), probably the best vis in Micronesia, relaxing drift dives in mild currents which make UW photography a pleasure. Some turtles, eagle rays, schools of barracuda. Kosrae is the youngest of the Caroline Island chain (made up of Kosrae, Pohnpei, Truk, Yap and Palau), so it has sunk the least. This makes the fringing reef much closer than the other islands. Boat rides with us are 5 to 25 minutes to world class sites, as we have boats at two different harbors, so we can choose which to use each day depending on the wind and swell direction.
Here is a link from our website with information about flights to Micronesia.
http://kosraenautilus.com/flights.html At the bottom of that page there is information about United Airlines "Visit Micronesia" discounted airfare. As mentioned there, it is not well known with United staff, so you might have to be persistent on the phone to them. This could save you $500 to $1000 on the type of itinerary that you are planning, as it is designed for multiple island stops.
I hope I have been reasonably unbiased with my comments, but it is hard when you are passionate about what you do. Good luck with your planning, and I hope you have a very enjoyable trip to Micronesia.