There's 3 main reasons why Fire Emblem fans dislike Roy. Note this basically only applies to Western fans, since in Japan Roy and The Binding Blade are among the most popular Fire Emblem games there.
===
1. Roy's characterization. Roy is stoic, especially quiet, and doesn't exactly talk much to carry the plot. Part of that problem is the translation isn't particularly great in spots. He's also very young, at the age of 15, and is one of the youngest Lords in Fire Emblem history.
Another part of that dynamic is really in Fire Emblem 6: The Binding Blade we got the first game where the entire ensemble cast really had a more intricate role in the plot. Sure in 4/5 we had a few moving Lords and other highly characters, but everyone else feels largely just like another face in the crowd. Roy didn't get enough screen time because of that transition, and it ultimately hurt his characterization and character development. Intelligent Games tried to make the rest of the cast matter so much that Roy wasn't the main character of the manga, but rather a manga original character, with different characters basically "taking over" various chapters.
In a proper remake of Fire Emblem 6: The Binding Blade this would obviously be alleviated through some means. Intelligent Systems have in later Fire Emblem games since employed methods that keep the main characters in the spotlight while not make every character feel like a face in the crowd.
===
2. The second main reason Western Fire Emblem fans dislike Roy is he's fairly underpowered (although in the end he can easily be super insanely overpowered). He's not exactly terribly helpless and weak throughout, but he can be at parts. Western Fire Emblem fans are backwards group in a sense. Many of the dedicated Fire Emblem fanbases' favorite characters are the overpowered ones, and their least favorite ones are the underpowered ones or even balanced ones. Hector in Fire Emblem 7 for instance is very overpowered, and yet Western Fire Emblem fans almost universally praise him when discussing balance. Among dedicated fans of other series, as well as most Japanese Fire Emblem fans, the inverse is true. They loathe these sort of imbalances.
Aside from a few overpowered units, Fire Emblem 6 has a pretty balanced cast. You really have to think to win, when compared to 8 you can basically do no wrong. Newer fans are put off by this, and again, long-time fans don't like this, especially since the challenge starts early. Fire Emblem 7 doesn't even begin to get remotely close to hard until the game is 2/3rd's over.
Roy actually functionally is very different from most Lords. Since he's so young, he's kind of weak and fairly inexperienced. He kind of serves a Tactician-like role, but still he must be strongly protected. You can't just YOLO with him like you can with say Robin, Hector, or tons of Fire Emblem 8 characters (well not until the end if you level him up right and RNG grind).
A few people earlier in this thread used a chess analogy with Roy where he's like a king early, and how late in a game of Chess the King becomes really powerful. I like to think of it more like say a boxer. In boxing you don't just go and plug anybody against a world class boxer, you go through the amateurs, then the bar boxing scene, then the clubs, then the bigger clubs, then big regional shows, and then you start making it in prime time. Roy starts off as basically an amateur boxer surrounded by potential pro opponents. You gotta scare off those potential opponents with more experienced units, build him up against similarly experienced boxers, and gradually keep allowing stronger and stronger enemies to fight him and protect him from much better boxers less and less. Eventually when he gets the Binding Blade though, he often becomes really good and sometimes even essentially invincible.
===
3. Western Fire Emblem fans want their favorite Fire Emblem characters over Roy. Look at all the speculation "waifus of the week" that go out of style whenever they get "old" or "something new and trendy comes along." Many of these people think Smash should have these minor characters like say Lissa or Anna instead of just the main Lords and Tacticians.
There's also people who would prefer Lords with original or different skillsets and movesets, like Hector, Chrom, Lyn, and Sigurd. Some of this logic can be kind of faulty, since clones and semi-clones, especially veteran ones, aren't directly competing for time, resources, and "slots" for a spot on the roster. And if they were, we wouldn't have Lucina and Robin both playable in Smash 4.
\\