Hi
Im diving in Ponta and Sodwana almost every fortnight so I think I can answer your question.
It all depends on the charter you choose that will make it a good diving experience. The south of Mozambique is very close (+-40km) of Sodwana bay. (Both Tropical). Therefor the sea live is more or less the same. However I do find that the diversity on Sodwana is far better than in Mozambique, especialy in the micro life category.
It also depends on what you want to see. In Ponta (Southern Moz) youll find a worl renowned sight, Pinnicles. Every 9 out of 10 dives I found Zambezi's sharks (bull shark) and eagle rays. Other possibilties include schools of 100 hammerheads + (ive seen this in April), manta's, and the occasional Tiger shark. Its a deep dive - bottom at +-35-42m.
Northern Moz is awsome and unspoiled but you need a 4x4 vehicle to get there and is +- a 13 hour drive from JHB intl airport if you lucky. This I will recommend if you want to stay for 7 dys or more at one place.
In South africa the reefs is as diverse as the culture. Starting with Sodwana which is a marine protected area. Its tropical and the number of species (if you use a good charter) will blow your mind. Almost gaurentee a swim with a whaleshark if you stay 4days + and visit the outer reefs. Then further south you get Aliwal shoal (semi tropical). Gaurentee sightings of a number of shark species, can be very dangerouse dive if the conditions is not right. Recommended for advance divers with +40 dives. On a nice day anybody can dive but conditions can change quickly. There is also a massive wreck here.
Further south you can dive great whites and other less visited sights. Example Knysna heads for sea horses etc.
Will recommend the following ratio. 2 days aliwal for sharks, 4 days Sodwana, 3 days Ponta for pinicles and other reefs. They are all +- 2 hours drive from each other.
OR
7days in Northern Moz
Cheers
