I couldn't agree more. A live-aboard is definitely the best option.
By the time you have paid for meals & drinks at the PPRT for a week, and tried to cram in as many dives as can be done from a live-aboard (pretty much impossible!) you will have paid more money than going on a live-aboard. Also, a lot of the dive sites, particularly those around Ngemelis & German Channel (and let's face it, 99% of the day boats go there on a daily basis!) are an hour away from the resorts. Why spend so much time getting to a dive site when it's a 5 minute tender ride from a mothership.
I woud recommend Ocean Hunter if you like small groups (6 max) only snag is what if there rest of them are dorks!
The Aggressor is nice, and it is a shame Sun Dancer ha smoved to Belize as I don't much go for Star Dancer and she is only there 6 months o the year, as she splits her time between Palau & PNG.
If you did decide to go hotel based then the PPR is the best, but they have an arrangement with the Caroline Resort whereby people staying there can use the PPR's beach & facilities. When the resort is full service can be a tad slow, however. And if you are there for any length of time then the menu gets a bit boring aftr a while. Other hotels that are cheaper but less "resorty" in feel would be Sunrise Villas and perhaps the West Plaza Coral Reef. I would not recommend the Palau Marina as it backs on to the municipal dump!
I would also use NECO Marine for day diving. They would pick up from the PPR dock. By the way, Scorpionfish, Splash is the dive operator at the PPR; Photo Palau is the photo place. I would not use Splash as a dive operator for all the tea in China. There boats are too big and they mainly cater for Japanese divers.
You are right about El Nino, though. I went pre and post, and post the reefs are in a terrible state, though obvisouly the soft & fan corals are still fine. Ngemelis Wall is still amazing, but the hard coral gardens that were so beautiful in Palau have all gone now. Yap has currently got better reef diving than Palau as it managed to avoid the worst of El Nino.
And as for sharks. Well, having done dozens of dives at Blue Corner I can safely say that the best shark encounter there came nowhere near as close to the "average" shark encounters I had in Tahiti in October. See Part 4 of my Tahiti Trip report on this forum for more details! But you won;t get any interesting coal in Tahiti. Just loads of fish!
If you want to see what Palau looked like in the good old days before it was blighted by el Nino, click here!
My Palau images
If you want great fish life & fab reefs my advice is go to PNG.