Having done both PADI and SSI I have found the biggest differance is the actual Instructor.

The Instructor can be certified by all the organizations, but if they suck as an Instructor it doesnt matter.

For me I prefer SSI, but thats becuase it works out better for my schedules, I like the dive shop, the people, the Instructors, and the dive location they are at.

By the way, if youe ever in IL, I would highly suggest diving at Mermet Springs (Thats my shameless plug for them!)