I think the whole connection involving the Hero of Time and The Hero's Shade is that MM Link got stuck in the Lost Woods after saving Termina (and if OoT is correct, people lost in the woods get turned into a Stalfos). Meaning, he was unable to pass on his skills/experience due to traveling the lost woods for so long.
Granted, it is likely MM Link mastered the ability to transform (as he had plenty of experience in MM to understand how that works), explaining why Hero's Shade can turn into a Wolf (maybe a form MM Link gets latter on a on another adventure after MM?) and Link just uses the Salfo's form to better use sword attacks and what not :l.
I think that a third game in the Hero of Time saga could potentially explain this better but as is, it is easy to assume that MM Link got lost going back to Hyrule and ventured off into another land, solving that crisis and 'something' preventing him from coming back to Hyrule :l.
Either way, it is fun to speculate what happens
.