Hi hq-
You are comparing apples and oranges here. Molokini is a visually spectacular dive with lots of reef fish, near 100% coral cover in places and as a result, probably the quintessential dive if you are on Maui. It is also fairly benign with visitors ranging in skill level from snorkelers with lifejackets to fairly advanced divers drift diving the back wall.
By contrast, Molokai is all about hammerhead sharks. You might also see tuna, dolphins, and galapagos sharks, but the hammerheads are the star attraction. It is also an advanced dive. You will be dropped off effectively in the middle of the Pailolo Channel which, even on a nice day, is much rougher than most days at Molokini. The ride to and from Molokai generates a lot of lost lunches.
Which is better all depends on your preference. I prefer Molokai because even when I am photographing a macro shot, I am always hoping in the back of my mind for something larger. I dive for a sense of excitement and adventure and am usually pushing my boundaries, and in this light, Molokai fits the bill. If you prefer relaxed diving with beauty all around, Molokini is the way to go. Either way, have fun!