The way I view projectiles is that they are methods of positioning your opponent in an odd place so you can approach easier. In M2's case, I see a shielded SB as a reason to go in because you know the person can jump/aerial OOS, spotdodge, roll, or WD. 4 of those 5 options are defensive ones so you don't really have to worry about them in terms of being punished for this. What you would have to worry about(this is assumed to be spaced so no grab btw, you could space it to look like you're about to be grabbed though but that's a different story) is the aerial OOS.
Now then, since it's Ganon, you can expect a retreating Fair most of the time, or maybe a Dair if you're on top of him. Either way, you have time to WD up, tilt(at least Dtilt but maybe Ftilt/Utilt too I dunno) then WD back before he can attack, then WD back in to punish him(spacing out his safety jab probably).
Seems safe enough, as it's pretty much what any character with a tool like that would use on Ganon.
Now then, he'll catch on and start attacking before you get there. You can now start WD'ing early instead of SB'ing and attack (probably with Utilt since he'll Fair).
Now he's afraid to attack so he shields. Do a little WD/DD tricks mixed with SB to control(but only 1 imo) and work in your grabs, as anyone who plays M2 frequently will realize that his WD is incredibly fast when combined with his tilts, but he can be rather easy to punish OOS if he becomes predictable.
Of course, you also have WD jabs. These can force a shield grab when spaced close to your opponent and their quick cool down time can lead into Nair or Fair or a grab or whatever if you get a good reaction. If they continue to hodl their shield, try for the grab. If you get Daired out of the grab attempt then work on movement after the jab or getting a tilt in or even doing a quick DD to make sure your opponent won't move.
SBs can also keep shielded opponents from jumping as you approach. While not necessarily amazing sounding in theory, the ability to not jump OOS does worry some people, but realistically it cuts off a very good escape option, leaving you with a stronger mental hand in the situation.
Does that help?