I think it was SuperBot's idea of variety (as someone above mentioned) and individuality. If every Level 3 Super was a screen-clearer, well that wouldn't be very exciting, now would it? But as a result, some Supers are superior than others which is the difference in balance.
But at the end of the day, every Super has its advantages and disadvantages.
That's very true. Spike's level 3 being a screen clearer is not something I want to rely on in a timed match, but in a stock match, it's a good way to clear a life from everyone without much effort on my part since he builds AP with incredible ease. Also, in a 2v2, his level 3 is good just because if my partner is taking lives with their level 1 and 2, then I can just build up to 3 and finish things up with one deciding GUARANTEED kill on both members of the opposing team.