"Mary Sues" also tend to be characterized as being so perfect, they're non-existent characterwise. Meaning, their character is so blatantly obvious, one-dimensional and very predictable because they have no perceived "flaws."
So far, Tendou is falling just short of fulfilling that last bit. Shoichi, on the other hand, is not a Mary Sue. You want to create characters that are like Shoichi - perhaps a bit of an expert in everything, but you want to stay away from Mary Sues as that leads to rather stiff, predictable, uninteresting, stereotypical plots. Not that using Mary Sues are wrong, they're just not as interesting and dynamic.