Calling them the Shadow Dragon and the Divine Dragon as nicknames the Alteans had for these specific powerful Pokemon is OK. Their exact species would not have been known.

While the personal conflict between the Alteans and the Shadow Dragon may be explicitly a force of good vs. a force of evil, the overall conflict enveloping the world would not have been like that. When Marth left Altea to see what was going on elsewhere, he would have become conscious of this. You may add clarification or rewrite that portion as you feel necessary so long as this is extremely clear, as the premise of the game relies on this point.