I have ran both. When it comes down to it, it really does not matter both tuners are great. I swapped to Diablo and a Mafia from all SCT just because Adam from ST can get a better tune for my Procharger with that system.
SCT seems to tune better on twin screws it seems and Diablo seems to tune better on centrifugal from what I have seen. Most of the major drag cars you see that are Centrifugal seem to be diablo tuned.
As for minor bolt ons it doesnt matter which one you buy they will all be the same because you will just be loading a tune that some one else makes for you. Unless you are changing things on your own like some advanced people might do then personal pref will take in effect.
Now a few years ago SCT blew away Diablo because Diablo could only hold 1 tune so nitrous guys had to redo there tune by them selves every time and keep pads of paper with the changes they had to make on them. This was 04 and Below. For us the Diablo will hold 5 tunes.
One plus on SCT is that it has a Two Step but I plan on buying the MSD two step I heard the MSD one works better then how the SCT one works. Not sure how just things I have heard.
The best thing you can do that will save you the most money. Is call around your local tuners and see what they tune with. What they tune best with because once you get past the point of having to have a can tune and need custom dyno tunes they might want to you swap to another tuner from the one you have. So you might as well get what they work best with and favor.