Lucky you!
Having been to both, I'd go back to Komodo in a heartbeat.
In Palau, I did the EcoExplorer. I think her refitted sister ship the Big Blue Explorer is there now instead. They are much less expensive than the Aggressor or Ocean Hunters but I still had a great experience and Asian style BBQ every night. The company seems to operate out of the Philippines and the crew were fantastic. My impression was that most liveaboards moor or stay near in German Channel most of the week and maybe make a trip to Ulong/Peleliu at one point. It was my first time to the Pacific. The diving was fantastic and there were, as advertised, so many sharks at times I didn't know where to look. Blue Corner, Ulong Channel, and Peleliu are amazing for the sheer quantity of fish and pelagics. There is some current and it was mostly drift diving with the chase boat trailing. Definitely glad to have had experience with current before making this trip. Palau is quiet, despite associations with the US (USD and English widely used) most tourists seemed to be from Asia (esp. Japan and Korea, no surprise given history and proximity) or Europe. Palau is quiet with lots of history and I enjoyed talking with native Palauans in the evenings on either side of the trip.
In Komodo, I did the Mona Lisa, out of Labuan Bajo and ending in Bali. There are lots and lots of liveaboards to fit all budgets in Komodo and there are plenty of budget options. You need to be a little cautious as some of them looked as though the divers might not enjoy the experience. I would have gone with Grand Komodo but it didn't look like the dates would work out. Because of the currents, you will get the most out of the trip with DM and captains who really know the area who mostly work for the companies who operate in Komodo year round. Some ships come from Raja Ampat or other countries in Asia, but I am biased for the Komodo-based operations which work do a lot of work to protect the marine park and sustainable tourism. You could ask around about the good dive ops or work with a local agent in Indo as there as there are a lot of ships which do mostly full charters but might have a slot or two. The crew were Indonesian but the DM's from Europe or the US.
I also recommend against the trips which have to travel to or from Bali as the best diving is in the heart of the part and going to Bali just means you spend fewer days where the best diving is. Many areas outside (and inside) the park have been have been bombed with dynamite esp. on the route to Bali. YMMV, but we dove from a tender which did follow during the drift dive. Water was much colder and currents very tricky, but I don't know if I will ever see that kind of diversity and quantity of marine life ever again. I didn't get to dive the south, but one dive on Castle Rock made the whole trip worth it. The fish were so thick I could not see through them -- until the dolphins came. There really isn't much in Labuan Bajo (and I didn't spend much time there), but there are plenty of regular flights to/from Bali. Indonesia was definitely cheaper than Palau.
Either way, you will have a fantastic trip. Good luck with your decision!
Yeah, kind of pricey, but it is a two-week trip.
