Until you get to the divemaster level, the recreational courses are basically interchangeable between the agencies.
The instructor you like is way more important than the agency the instructor teaches for.
Small exception: if you are a card collector, determined to get PADI specific Master Scuba Diver, then the 5 specialties you do need to be PADI specialties (who you do advanced and rescue with does not matter). I think SDI does not care, and I think SSI has some limit on how many can be non-SSI.
The instructor you like is way more important than the agency the instructor teaches for.
Small exception: if you are a card collector, determined to get PADI specific Master Scuba Diver, then the 5 specialties you do need to be PADI specialties (who you do advanced and rescue with does not matter). I think SDI does not care, and I think SSI has some limit on how many can be non-SSI.