Maumere actually has some great dive sites, Pomana, South Pangabatang and Babi are all excellent dives for soft coral scenery with some great critters on them as well, pigmy sea horses, leaf scorpionfish and more... The scenery on Pomana is very stunning, though only in one main area, this area has been heavily impacted in certain areas though there are really gorgeous spots. There are always quite a few reef sharks, large Napoleon wrasse and good schooling fish action on a few sites as well. Then for critter diving, there is onyl really one place to head for Wodong, this area has excellent critter diving and a very interesting little wreck too! If you go with someone who knows the critter site you will really enjoy this dive and want to dive it over and over again. The main issue with Maumere is one of accommodation, all the hotels there have been left with little or no income for a long time, they are all very run down. The only operator worth diving with their for land based diving is Anchermi, thoguh this is kind of primitive, simple grass huts, thoguh great friendly and realxing vibe, they use local fishing boats, diving there is fairly cheap. The main thing do not expect 5 star service or comfort. Oh yeah in season they even have dives where that regular see hammerheads as well!
The best trip in this region is Flores and Alor combined, there are fantastic reefs on the far northern area and islands north of Flores and to the east Lembata has a place where I have personallu been seeing lots of big fish action, hammerheads and plenty of other sharks, the reef scenery is outstanding, so much so that on the last trips through here divers requested to dive the site again. Then you get into Alor, the big issue with ALor is one of operators going to the sites in "The guide book". This is now very out dated, Sharks Galore and Kals Dream do not always perform and for shooters are next to useless, I ahve yet came across a shooter who ahs taken any decent images of any big fish or scenery from these sites. For me the real essence of Alor is critters, wonderpuss, mimic's rhinopias, frogfish and ghost pipefish in numbers you loose count of, check outhttp://www.diving4images.com/flores_alor-gallery06.html to see a very recent gallery from this route.
Check out the new resort on Alor, I know the guy who runs it and he has very good reputation from his time up in the Togian Islands, Sulawesi area where he directed a small live aboard. His site can be viewed at http://www.alor-divers.com for more about a good operator on Alor, he is not really mad into his critters, though he really knows the best reefs for fish and scenery.