So much good advice - thank you everyone who has written so far.
Luko - thanks so much for chiming in (I have read many of your posts, and enjoyed your terrific photos). I was worried about viz as well. I am leaning towards Dec 2013 over Summer 2013 as I agree, if I am going to make a special trip to Ambon I definitely want to 'do it right'. Yes, I absolutely considered Alor but the 1 liveaboard I found diving that itinerary this summer I did not have an outstanding experience on last summer, so I am passing on that. I almost made an Alor trip last summer but it didn't quite work out with dates. It's on the list but not as high as Ambon

I know nothing about Alor or Bandanaira land-based diving - but would be interested to hear about them.
instructorinasia + ocdiver1 - thanks for the thoughts on Lembeh. Interesting to hear about the Rhinopias, oc. When I was in Lembeh in Aug 08 I was told it was not the right season for flamboyant cuttlefish (which I have still never seen) and a number of other critters. That was my first visit, and the comments of only 2 DMs at the small resort I dove at, so I didn't really know what to make of it all. I tried to search for the seasons of Lembeh critters - would be great if there was a site with broad ranges of animals like someone did for the Red Sea.
ocdiver1 - in their new location, Maluku now stays open all summer (high season for European tourists). As Dom mentioned they have a discount on room rates (but not on diving) in the summer.
All - I also had a great chat with Andy at Maluku about summer conditions - seems like a great guy, very professional and he summarized both the pros and cons of his experience last summer in particular. Mother Nature being what it is, it's hard to predict.
Raja/Ahe/Cenderawasih are not in the cards for me this summer. Dom I do have the specs on all the itins you mention already (have dove a slew of diverse ops over the years).
Re the Maluku frogfish, if anyone has any advice on seeing one, would be great to hear. I did not realize how rare they were, since I have seen photos from people who were only in Ambon a couple days. My thinking is that a longer stay would increase the odds of someone finding one.
N