Bottle Inn is still quite good, in my opinion. The menu changes often and the service is still quirky, but the food can be delicious. When they have their seafood specialities (Lobster Pasta, Seafood Ravioli) or their Short Rib Pasta, it's really quite good.
Also a plus: They let you bring your dog for outdoor eating and the heat lamps keep you warm.
What kind of food are you looking for? I like Michi and Cafe Pierre for somewhat upscale choices. Former has Asian Fusion and latter is California-French. Mama D's is good for really casual red sauce Italian. Rock N' Fish is pretty good for fish--more expensive than Mama D's, but less expensive and more casual than Cafe Pierre and Michi. Coco Noche is also good for a fun experience with wine and chocolate tasting, and a small selection of Asian-inspired tapas. I think Avenue is regarded as the best restaurant in Manhattan Beach, but I've actually never eaten there. Never been to Bottle Neck.