All three sites (Mabul, lembeh and Northern Bali) have only weak currents.
Lembeh has, IMHO, the best critters but a muddy bottom that is easy to stir up - you may not make many friends with photographers in your group if your buoyancy and fining isn't good. could potentially go down to 25 metres + but plenty of stuff in the shallows as well. Most people who dive here are photographers, but the diving is easy (if a little colder than the other two).
Mabul - sandy coral bottom with relatively shallow dives to see frogfish, ghost pipe fish etc. Most operations dive Sipadan (deep walls with lots of turtles and moderate currents) in the morning and Mabul in the afternoon. Fine for beginners.
Seyraya/tumbalien Bali - sloping black sand bottom with isolated rocks hosting coral and a variety of unusual critters. Can go as deep as you want, but plenty to see above 20 metres. Also fine for beginners.
Cheers,
Rohan.