Roy should definitely stay in. I see no reason to take him out and I can easily see Fire Emblem getting four representatives. I mean, hell, the series is 17 years old and has ten games out, technically more if you count the BS FE series. It created an entire genre of video game. Give it some love.
As for Roy staying you have to realize this. A character does not simply represent his, or her, self. A character also represents its game.
So with that I'll give you my reasons as to why Roy should stay.
1. Roy was the first portable Lord. This is a fairly well known fact. Hell, a similar reason was used for Ike.
2. Roy's game is the third highest selling FE game. Getting near 500K in sales puts it just behind Fire Emblem: Seisen no Kiefu and Fire Emblem: Monshou no Nazo, FE4 and 3 respectively. That is no small feat.
3. Tying in with reason number two. Roy revived the series after the marketing blunder that was Fire Emblem: Thracia 776, I'm not saying anything about the quality as from what I hear it is a very good game. FE5 was released at the very end of the SNES's life cycle, in fact it was the very last game to be made for the SNES, and even faced with that they decided to sell the game exclusively through Nintendo's online store.
4. Roy's game introduced a few things into the series as well. The major thing that happened was a revamp of the magic system changing it to the Anima/Dark/Light triangle that we have now. This is the most used magic system throughout the series, and considering its a giant chunk of the game it shouldn't be taken lightly. Another thing is the introduction of the Support system.
Now one reason I see people against Roy is that he was an "advertisement". While that technically may be true, he did appear in Melee before his game was actually released, what would you say if I were to tell you his game, known as Maiden of Darkness(Ankoku no Mizo) at the time, was originally for the Nintendo 64. It was then moved from there to the Gameboy Advance and underwent a name change shortly after.
Another that I see is that Roy is a clone, or at least accused of being one. Well, both Roy and Marth need changes to there move sets as some moves fit one of them while the others don't. I present to you my Roy moveset!
A - A straight horizontal slice starting from the right and going towards the left.
AA - A straight horizontal slice starting from the left going towards the right.
AAA - A vertical slice going from the top down with the sword on fire.
Over + A - A vertical slice starting from the top and going down. Roy also ends up one step forward after using this attack.
Smash Over + A - A vertical slice starting from the top and going down while ignited on flames. Roy also ends up one step forward after using this attack.
Up + A - Roy shoves the flatside of the Sword of Seals into the bottom of the chin of the person he is attacking. If timed correctly it could be used to block an attack.
Smash Up + A - Roy shoves the flatside of the Sword of Seals into the bottom of the chin of the person he is attacking, while the sword ignites into flames. If timed correctly it could be used to block an attack.
Down + A - A vertical slice starting from the bottom and going up. This attack will knock the enemy up into the air.
Smash Down + A - A vertical slice starting from the bottom and going up, while the sword ignites into flames. This attack will knock the enemy up into the air.
Crouch + A - Same as Melee.
Aerial A - A simple forward kick.
Aerial Forward + A - Same as Melee
Aerial Backward + A - Roy kicks behind himself.
Aerial Up + A - Same as Melee.
Aerial Down + A - Roy's swings his leg forcefully down hitting with the heel of his foot.
Grab attack - Roy knees the person he is holding in the gut.
Forward Throw - Roy rams into his opponent's chest with his shoulder.
Back Throw - Toss the person you're holding behind you and kick them in the chest.
Up Throw - Roy tosses the person he is holding into the air.
Down Throw - Roy puts his foot behinds his opponent's and shoves him to the ground.
B - Hono no Dansu/Dance of Flames: Roy goes into a three attack combo with the Sword of Seals on fire, each one slightly stronger than the last as the Sword of Seals reacts to Roy. Similar to Roy's Double Edge Dance from Melee.
B+Over - Blazing Slash: Roy will pull his sword back while it is igniting then swing it over his head sending a fiery orb forward that explodes after it goes a certain distance* if it doesn't hit anything. While Roy is in the air the orb goes down and forwards at a shallow 30 degree angle.
B+Up - Rising Phoenix: Roy jumps up into the air and comes back down at a 30 degree angle with the Sword of Seals, on fire, pointed forwards in front of his body.
B+Down - Reinvigorating Flame: Roy takes a defensive stance. When Roy gets hit with an attack while in the stance fire flares up around him for a second and he heals for 3/4ths of the attack power and knocks back the opponent while dealing 1% damage. Only works once per stance.
* - Slightly shorter than Samus's missile range.
As you can see it is lacking a Final Smash. However, I present to you that as well.
Final Smash: Hartmut's Legacy
Zephiel comes onto the field with his sword Exaacus and starts fighting alongside Roy. At the end of the duration of the Final Smash Zephiel leaves while performing either his ranged critical or his normal critical, depending on how close the nearest enemy is.
I think this Finals Smash works great. The name comes from the fact that Zephiel's Exaacus and Roy's Sword of Seals both belonged to Hartmut, founder of Bern. Also, despite what you might think of Roy working with his enemy, you have to remember that neither Roy nor Zephiel held any contempt towards the other. Roy saw Bern attacking neighboring nations and wanted to end it and Zephiel had a misguided goal thanks to his father's numerous assassination attempts on him.
One thing you'll notice about Roy's A move set is that his smashes are copies of his normal attacks just with fire added onto them. There is a reason for that. Those are his critical attacks. You could tell when Roy pulled off a critical with the Sword of Seals because his weapon would ignite.
Roy's neutral B is derived from his conversation with Jahn, one of the original dragons, near the end of the game. Jahn explains to Roy that when Hartmut went to slay Idoun the Sword of Seals reacted to his emotions, and instead of killing Idoun it simply sealed her away.
Roy's over B is derived from his ranged attack with the Sword of Seals. Hopefully that one was obvious.
Roy's up B isn't really derived from anything as the only thing Roy has similar to what a normal up B would be is his amazing jumping ability after he attacks with the Sword of Seals.
Roy's down B is derived from the Sword of Seal's ability to heal Roy.