No, there's no significant difference.  The difference is in the individual
instructor, not the agency.  Watch out for pushy gear sales before you're
ready to buy (i.e., before you're certified and somewhat experienced).
Watch out for weekend express classes.

Lots of people will be telling you that it's the instructor that counts, not
the agency.  I agree.

Having said that, all else being equal, I'd chose SSI over PADI pretty much
every time.  These are all corporate issues, not instructor or diver issues.
Here they are:
1. I don't have a PADI certification, but my wife does and I've sat through
some of their courses.  PADI pumps PADI, strongly and heavily.  In my
opinion, their marketing program is a higher corporate priority than their
training programs.  That doesn't mean that they don't offer quality
training, but it does mean that theirs a strong incentive to give a higher
priority to graduating a student than to ensuring he's competent before he
graduates.
2. In my experience, PADI is more course oriented, SSI is more skill
oriented.  This varies with the instructor, but on the whole, I've found
more focus on practicing skills with SSI than with PADI.  This, in my
opinion, is one of the biggest reasons that SSI grew quickly in the US
despite PADI's far larger and better financed marketing department.  I, and
most experienced divers, find practicing skills to be one of the more
important factors leading to becoming what others recognize as an
experienced diver.
3. PADI has a strong tendency to ignore anything that does not come from
PADI.  SSI and some other agencies I have experience with are more likely to
present contrasting views and alternative methods of addressing the same
issues.  While it's important to be certain that each graduate knows some
way to address each issue, it's usually considered better for them have
options to chose from or, to form a basis for a method or style of their
own.  Divers trained to think for themselves tend to become better, all
around, divers than those that are trained in a more dogmatic style.
4. PADI tends to teach their way as rules.  SSI and most other agencies tell
it like it is.  They teach guidelines, explaining the whys of each
recommendation and encouraging the individual diver to decide what his
personal rules will be.  I got a real life example of this, this weekend.
Before the dive boat left the shore, the Captain went over a set of rules.
Each one of them started "PADI rules require . . . "  It mattered not that
at least one of the divers on the boat, me, has no association with PADI at
all.  The rules included "no decompression," "no penetration," and back on
the boat with a minimum of 500 psi remaining.  Kind of silly when all but
two of the people aboard are clearly geared for more technically challenging
diving.  To the Captain's credit, nobody pushed the issues.  They chose not
to notice my very obvious and well marked tank of decompression gas or the
spools of line both my buddy and I were carrying.  Still, he preached PADI's
rules because PADI told him he had to.  He may have to do what PADI
corporate says in order to advertise himself as a PADI shop, but PADI is
over the line when they try to impose their rules on anybody.

Despite all of that, the instructor is still important than the agency.  A
good PADI instructor will provide good dive training.  So will a good SSI
instructor.  Either certification will be recognized world wide.

Lee
YMCA entry level
NAUI Scuba
SSI Advanced, Deep, Navigation, Stress and Rescue, Master Diver
TDI Nitrox