Having CX is a great option don't get me wrong (granted no F). My wife and I went here for our honeymoon last Oct and had to take BA to AUH then EY to MLE. I remember the MLE-AUH flight being late and staying at our hotel a while longer wasn't a huge issue, I think we might have had to pay a minimal fee.

Also, most decent resorts that are within speedboat range have their own private boats (ours was free). The main issue is wanting to get your dream vacation started off with such a late arrival. Personally I wouldn't want to have to overnight in MLE, no way. For most US based flyers, EK or EY are the way to go.