PADI is the way the world learns to dive, so if you're looking for work in different islands, PADI would make you the most marketable.
NAUI is the better choice if you want higher standards and total academic freedom to structure your courses your way. I have made a lot of changes within the normal scope of diver education through NAUI, which has allowed me to teach my students use of a more modern equipment configuraiton, incorporate different breathing gasses into recreational specialties and more.
NAUI has also been great at coming up with courses of value (ie Wreck External Survey and Penetration, Master Scuba Diver vs. just swimming 4 times around a shipwreck and becoming a "wreck diver", or taking 5 specialties and being called a Master Scuba Diver).
Do your potential students want a course that is a little more involved, or do they want a course that requires the least amount of instructor/student contact, minimal hours and fewer open water dives?
I believe certification is earned, not bought.
SSI is an incredible marketting agency. They support their dive stores 110% and the students benefit from this support as well.
SDI has come on very strong the last few years as well. TDI/SDI have combined now become the 2nd largest agency in the world if you combine the tech and recreational agencies as 1.
There is always the agency vs. instructor debate. Yes, you will make your courses either par or above par, however, you want an agency that is going to support you and work with you, not against you.
You want an agency that you can have a good line of communication and can call upon in your moment of need, should you require anything.
All the agencies have customer service staff to assist in this.
The regional sales rep or regional managers are there for you as well, should you have questions.
It certainly won't hurt you to have a couple of agencies to choose from.
Start with one of the main agencies and see where your interests shift from there.
Good luck.