Scraggy can't plow through the most of the game given that his initial offense without moxie is just barely mediocre. Team Plasma also has slightly better team diversity that doesn't scream "just murder me with HJK already" (although it still does).
Mag is fine in Top imo: he has only 4 non-resists, 3 of which can be solved by just putting a water-type on your team, giving you great defensive synergy (Fighting and Ground aren't resisted by a Magnezone + Samurott/Azumarill core, though the latter may as well be a free win for the water-type). Coming very early, with a move that guarantees 2HKOs left and right, in an era without boosting crap like Swords Dance or strong shit like Flare Blitz. Gets two gyms to annihilate (Roxie, Skyla), Charge Beam to boost his excellent 130 SpA and act as a pseudo-Moxie for SpA, Thunder for excellent late-game offense and decent bulk too. The only bad spot in his level-up movepool is between ThunderShock and Electro Ball, and you get the Volt Switch TM to help cover it up. He can win battles that Scrafty cannot because of the resistances AND the good initial SpA, neither of which Scrafty possesses.