I recommend reading my two replies in this thread:
https://voyageforum.com/forum/vols-entre-jakarta-flores-d11469362/. You’ll learn about potential difficulties booking on some Indonesian airline websites, how to work around them, and why it’s safer to cross the island from east to west.
Suggested 15-day/14-night itinerary without diving, excessive snorkeling, with walking and sightseeing:
Ende or Maumere, depending on the shortest flights available based on your arrival day, 1 night.
Moni for its Kelimutu, walks through surrounding villages, and the option to spend a night in Nggela, 4 nights total. This duration will also give you a chance to try Kelimutu again if it’s clouded over on your first visit.
Riung via a same-day connection in Ende (don’t let anyone in Ende tell you there’s no transport to Riung—just leave Moni before 10 AM). Riung and its 17-island marine national park for snorkeling, 3 nights.
Bajawa with its ethnic villages and hot springs, 3 nights. You can use local buses (though they’re infrequent) for sightseeing—I did it this way—but don’t be in a rush. If your patience isn’t endless, consider hiring a driver or agency instead.
Ruteng, 1 night to break up the 8–10-hour trip between Bajawa and Labuan Bajo. Use the time to find a local driver to take you to the famous spiderweb-shaped rice terraces.
Labuan Bajo, 2 nights, including a day trip to see the famous giant creatures in the nearby islands.
That’s a total of 14 nights. If you actually have 15 nights, add the extra night to one of the above stops—don’t add another destination.
The next day (Day 15 or 16), fly back to Bali. There are direct flights with several airlines, unlike the Bali-Ende or Maumere routes.
All stops are connected by public transport.
For the trip to Nggela, check the few daily transports from Moni (round-trip is best for an overnight stay).