They are powerful in different senses. Both swords have their own "sweetspots", Marth's being the tip of his sword and Roy's being the handle. The sweetspot of Marth's actually sends the opponent further than the sweetspot of Roy's, although you are right that Roy's deals more damage. Marth is also far superior in the air, with much stronger attacks considering Roy can't "sweetspot" his oppenents in the air whilst Marth can. Roy does have the upper hand with B attacks though.
What I'm saying is while Roy's smashes can be very powerful, Marth's can be more powerful when sweetspotted. When they're not sweetspotted, I think they're about the same but I'm not sure .