You should consider posting this to the Maldives forum too. I've been to both on liveaboards, though not in Sept. They are somewhat similar. It would be helpful to know what you look out for or maybe what you want to see.
Mantas: Maldives clear winner. Its manta season and there are cleaning stations.
Hammerheads: BDE clear winner.
Sharks: Mixed. Maldives has baited shark dives in the south with a chance of tigers, BDE gives you a chance of the oceanic white tip.
Reef life: Slight BDE winner. Loved the big schools in the Maldives, but the healthier reefs in BDE has interesting and curious life like napoleon wrasses.
Corals: BDE clear winner
Crowds: Draw (Both are popular destinations)
Currents: Maldives. BDE often has drift dives, but Maldives has the stronger of the two.
Visibility: Draw (Depends on rain in the Maldives and wind and current in BDE)
Non diving related:
Culture: Maldives. They are generally friendlier and well intentioned. Egypt offers a higher chance of being catcalled and made fun of.
Price: BDE. Egypt is cheap and offers great value for money.
