EDIT: This sums up what I need to say much better than my words below:
https://www.youtube.com/watch?v=X504v3v3iqQ&lc=z131ujsrcrz5z5h0o22vudgj5w3vuhqbb04
Should link to a specific comment in the video.
Roy was only hated by a small niche of western fans who only care about map-clearing lords that make the games easy for novice players, not anywhere close to any majority. He is a well-liked character by Fire Emblem fans, especially in Japan.
There were many, many other choices for DLC. Roy deserved his win. Roy's popularity, how important he is to Fire Emblem (represents one of its biggest continents, its second-biggest system, the only FE veteran, balances out classic FE from modern since Awakening used to be 50% of FE's representation, many other things), how important he is to Nintendo, fan demand from smash players and constantly frontrunning DLC polls, and other things not off the top of my head due to sleep deprivation are why he's important in Smash and why he returned.
He wasn't in Smash to promote FE6, he was included because a Marth clone was needed in Melee, and he was the best candidate to stand out. He was planned for Brawl (several major indicators of evidence exist, notably within subspace trophy positioning and progress within data files compared to other forbidden seven) so I'm not surprised in the least he eventually came back with Mewtwo.
If you have any other qualms with Roy's inclusion, feel free to let me know and I'll shut them down as soon as I'm online again.