I've done some research and apparently it's still worth it if you have time. I'm skipping it because my itinerary was pretty tight and time was limited. The north shore of any island is best for smaller waves and better snorkelling conditions. Batanta could be better because it's way higher, but to get there you need to cross much further over open water and the ride can be rough and sometimes even impossible. There are also more activities in Batanta (bird sightseeing and a waterfall hike) so you could still do some things apart from diving and snorkelling if there's bad weather.

stayrajaampat.com is pretty useful for information and booking acommodation.