The Mk 16 has a flow rate of about 175 SCFM while the Mk 25 has a flow rate of 300 SCFM. So the Mk 25 has almost twice the performance of the Mk 16. But I'd challenge any diver to tell the difference between a Mk 16 and Mk 25 in a blind test.
In the real world, 150 SCFM is all you need in even the most demanding diving situation. If you are deep enough for the Mk 16's 175 SCFM flow rate to be inadequate, you are deep enough that you have long since switched to helium mixes which slip through regs better anyway, making a reg capable of flowing 175 SCFM of air more than adequate for well over 175 SCFM of trimix.
One advantage of the Mk 16, is that I have never seen one freeze up even in water as cold as 33 degrees. I cannot say the same for the Mk 25 which can encounter problems freezing up in water colder than about 40 degrees.
SP has a marketing philosophy that promotes the MK 2 R190 and MK 2 R390 as it's entry level regs, the Mk 16 R390 and Mk 16 S550 as it's intermediate level regs and the Mk 25 with the S550, G250, S600 or X650 as its top end regs. Consequently SP packages first and second stage combinations in this manner and encourages sales to entry level, intermediate and advanced level divers accordingly with the goal of getting 3 sales to a diver over the course of their career. If you stick with their packaging options, you are also essentially forced to go with a more expensive first stage to get a balanced and adjustable second stage and this maximizes SP's profits.
From that perspective, some dealers may feel they are doing a diver a favor by selling a Mk 25 with whatever second stage to them initally under the "if you buy the best, you only have to buy once" philosophy. SP sales reps are not big fans of that approach either for obvious reasons.
The truth is though that SP will sell any first stage with any second stage, all the dealer has to do is order them that way. You pay slightly more by losing a package discount, but you can still get very practical and excellent performing combinations like the Mk 16 G250 or Mk 16 S600 or Mk 16 X650 for far less than you could get the same second stages packaged with a Mk 25.
So if you are diving cold water or if you prefer the Mk 16 first stage and do not want to the non adjustable S550 or the unbalanced R390 second stage, ask your dealer to get you specifically what you want. And don't take no for an answer.