Smash is a tribute series, it should b paying tribute to Nintendo's history, not its own.
Is Smash not a part of that history? After all; without Smash the west would never of even got Fire Emblem. Originally Marth and Roy were going to be Japan only, and the majority of us wouldn't have known about the series at all.
Roy got exactly what he deserved, a sticker of him. He isn't very important to the Fire Emblem franchise, and I have heard fans say that he is a very boring character in his own game, unfortunately I haven't gotten around to playing his game yet.
His game saved the series over in Japan. It was basically what Awakening was during the Melee period; Fire Emblem wasn't selling so well, and his game turned out to be a huge hit over there. He was also the first lord to not live in the same continent as Marth had, allowing for more world building.
His inclusion in Melee also helped launch Fire Emblem into the west, and his father was made the first western lord as a result. Chronobound has some very good pieces about Roy which are worth a read. Like you, I didn't think he was that important before reading them, but apparently he's a huge deal in Japan, and his and Mewtwo's removals were the most comment complaint about Brawl.
And even if he wasn't, Roy's still more important overall to Fire Emblem than Sothe, who did get a trophy. So no, Roy didn't get what he deserved. At all. He didn't even get the runner's up prize of assist trophy, nor third place prize as a trophy, he got the wooden spoon prize of being a sticker.
I have never heard of Doc having files in Brawl and Young Link isn't all that important to the Zelda franchise especially when Toon Link already has the youth portrayal. MewTwo was important to Pokemon for being the first Uber pokemon and Pichu is a notable mascot of gen 2. Them having trophies makes more sense than Roy, Young Link, or Doctor Mario having them.
Within the source files of Brawl there was data found of seven scrapped characters that had to be left out due to time constraints. They were; Mewtwo, Roy, Doctor Mario, Dixie Kong, Toon Zelda, Toon Sheik(although you could assume it was Tetra, not Sheik) and "Pra_mai" which some people have speculated might of been Plusle and Minun.
Mewtwo is important, no one can deny that, but Pichu was so unimportant it was the only cut Melee smasher that was actually planned from the get go, if Toon Link is viewed as the updated Young Link. I think the trophy inclusion is more to do with it being an easy rip again personally.
Young Link is kind of more important overall than you're giving him credit though due to the majority of Zelda games starring a younger Link opposed to Adult Link. Doc is less so, but he was still planned for inclusion alongside Roy and Mewtwo as playables and was part of a hugely successful puzzle series.
So yes I would argue they all deserved a trophy more than the likes of fricking Jet the Hawk, Ballyhoo & Bigtop, Sothe or Starly.
Maybe they'll get a trophy this time round at least and you can read about why they're more deserving than you give them credit for.