Yea the Sphere-hate SS argument is a good point. Although, I suppose it also depends on how large exactly the devs make the sideboard (should the idea be implemented of course). I mean if you only had say 6 slots, I'm not sure if sphere hate would be the way to go. Also, not all sphere hate is created equal. I feel like the "50 damage to all x sphere" SS would still be a subpar addition against bigs and even quite a few mids, and the "deal 40 damage and lower your opponents x sphere by 2" SS would actually be kind of worse than Vol agni SS to be honest. With all the multi-sphering going on, Vol agni usually has the same result, with the added bonus of always draining sphere (unlike the sphere hate SS). They'd definitely see more use than they do now, though, which I don't really think is necessarily a bad thing actually. But yea the sphere hate SS is definitely something I hadn't considered before that could definitely be a potential problem.
I suppose pikeru's suggestion could be applied as well (a ban list), but part of the reason for the suggestion was to increase card usage for cards that were way too specific in nature. It's something worth considering though.
The suggestion to simply increase the file size is also an interesting one to consider. One of the interesting aspects of deck building though is creating a functioning deck with the restrictions put into place. If you could simply add w/e you want and play it whenever you want, that aspect of deck building is entirely lost. So increasing the size of the file has to strike a balance between making deck building interesting while still allowing the player to have different options during a match. I feel sideboarding better retains the decisions involved in deck building. Every time you sideboard, you have to decide on what to remove to make room for what you wish to add, keeping in mind that your opponent is doing the same. On the other hand, increasing the file size keeps the element of surprise in every game. That's not to say you can't switch around your SS line up or make changes to keep things fresh, but of course after a game your opponent has a better idea of what you're playing. Then again, one could argue that often times you already know what your opponent is playing given certain cues (like their LP, how they raise their spheres, their opening units, etc.). Both ideas have their merits, and they both could be added as different game modes to provide different challenges I suppose.