When I first started diving it used to be 2-3min at 3ms for dives over 10
ms. I believe the change to 5m on the SS stop was that it was an easier
depth to maintain don't know why the time was changed maybe to compensate
for the slightly extra depth although a lot of the articles you can read
suggest 3-5 minutes. Maybe the 5min came around because boat and tour
operators where being on the conservative side. PADI I believe recommends 15
foot and a 3min+. I always do 5 at 5 except if it is a shore with a gradual
slope up to the egress point.

The short answer is, "if 3 minutes is good the 5 minutes is better."

The longer answer is:

1) A 3 minute stop probably is "good enough" provided that you
  actually hold a depth of 5-6 metres and don't get above 4.5
  metres at any time on the stop

2) A lot of beginners that I have observed really don't hold
  their depth on the stop very well

3) the more time that you spend at around 5 metres at the end
  of a dive (particularly deeper dives) the better. At 5 metres
  you are still under 1.5 BAR absolute pressure but there
  should be a good pressure gradient between the nitrogen in
  your blood and the nitrogen in your lungs. Also, from memory,
  all of the decompression research agrees that a differential
  of no more than 1.5:1 won't cause bubbles -- staying at 5
  metres gives you time to off-gas and move towards that 1.5:1
  ratio. (And, of course, when you are at 1.5 bar absolute the
  pressure in your lungs can be up to 2.25 and still be safe.)

4) If it wouldn't annoy the charter boat operators, (and doing
  this definitely would annoy them) the ideal situation would
  be to ascend to hit 5 metres with about 60-70 bar and then
  sit at 5 metres until you get down to about 10-15 bar. This
  could mean a 5-10 minute stop or longer.

5) another technique that you might want to consider is ascending
  to 10 metres and stopping there for a minute, then moving on to
  5 metres for 5 minutes. The point of the 10 metre stop is
  2-fold. First, it is a chance to off-gas a little bit and
  reduce the gradient before you get to 5 metres. And second
  it gives you a "set-point" to get your ascent under control
  before moving the final bit to 5 metres.

The bottom line on all of this is that even if you are doing
"no decompression" diving, you are still decompressing on your
ascent. What makes "no-decompression" diving ND diving is that
there aren't any required decompression *stops*. The design of
the ND dive tables is such that the partial pressure of nitrogen
should never exceed the point where dangerous bubbles would form
if you ascended directly to the surface at a rate less than 18
metres per minute -- I'd actually recommend a rate of 9 metres
per minute. A faster ascent increases the chances of bubble
formation -- just like when you pop the cork on a champagne
bottle and suddenly reduce the pressure. If you carefully extract
the cork, the pressure is released a little bit slower and you
are less likely tho have champagne all over the bench top.

Again on the point of letting the pressure reduce slowly, the
greatest percentage change in pressure occurs in the final
10 metres of the ascent when you go from 2 bar to 1 bar.
Slowing the ascent rate in the final 10 metres is a really
good idea. Taking 2 or 3 minutes to ascend from the safety stop
is an excellent idea.

There's been some ongoing research about "silent bubbles" that
suggests that some bubble formation may occur in dives that are
made within the limits of the tables. (Deco and no-deco) But
people are not affected by the bubbles since they are small enough
that they don't block the blood flow anywhere. Safety stops
are likely to reduce the size and number of these bubbles.

Another point to consider with the charter operators is that
their business is based on divers going out and having fun,
not getting hurt and comming back to do it again. They are
going to promote the safest possible options since that's
in the long term best interest of their business.

The final point is that you can get bent diving within the
limits of the tables. All it takes is going close to the limits
and possibly an extra risk factor or two -- and you've
earned yourself a trip to the Alfred. (Our local hospital
with a re-compression chamber) So if a 3 minute stop is good,
then a 5 minute stop is better.

-Don