We always used to stay at the Presidente, but their price hikes and our need to get multiple rooms as our son got older led us to just go ahead and buy a house on the island.
If price is not an issue, it would be my first choice of hotel. I particularly like the location, including the fact that it's at Paradise reef and I've seen some really nice stuff snorkeling right at the hotel.
I've never dived with Scuba Du. As others note, there are several highly-regarded boutique operators who will pick you up at the Presidente pier and we've always used one of them.
It used to be a very good idea to join the Intercontinental Hotel group's Ambassador Club. It seemed expensive at first glance, but you got a free night that in itself was worth significantly more than the membership (as long as you used it someplace like the Presidente and not a Holiday Inn) and free guaranteed room upgrades. Since we no longer stay at any hotel on the island, I don't know if that deal still exists. However, at our first stay, we got a lovely oceanfront suite for the price of their cheapest room, and one of our nights was free.