I know they didn't put 5 chracters in brawl that were in Melee, And I've heared complaints here and there But out of those characters I can think of at least one good reason why they didn't put them in Brawl

Dr. Mario
Okay. Don't get me started on him. It's just Mario in a doctor costume and instead of Fire balls he uses vitamins. They put every character in The Subspace emmisary in and if he was here it would ruin the storyline unless it was Mario dressed like a doctor at certain points. He was a complete waste of time even in Melee and I bet he was just a last minute adjustment.

Young Link
Young Link was just Link except younger. Once again he wouldn't fit in the subspace emmisary. Besides, They've got Toon Link now and with him there's no point of putting Young Link in it.

Pichu
Okay in a way I can understand peoples complaints to Pichu being taken out but then again when you think about it he was just a smaller Pikachu who was a touch faster and hurt him self whenever he used electric attacks.

Mewtwo
Even I have complainted in the past about Mewtwo being taken out, But then again they have Lucario now and he has simillar controls and is cooler (Okay, that's my personal opinion) But because they took Mewtwo and Pichu out they got to put Lucario and Pokémon Trainer in brawl. So I'm not too upset.

Roy
Okay, I have a bigger problem with them taking Roy out then anyone. Last night I started playing Fire Emblem Binding Blade and I've come to like Roy ever since I started using him in that. But He did only have one game (Marth only had one game too but it's been remade and is going to be remade again, But he's classic)
and Ike has had two and as far as I know is a much more popular character.

Honestly if they make a fourth Smash Bros I would be glad to see Roy and Mewtwo in it but I couldn't give a care about the other 3.

If you ask me, Roy should have been kept in, and not Ike, cuz Roy did more damage and was (maybe, I don't remember) faster. Mewtwo's loss was only acceptable cuz they put Lucario in, who had similar controls/moves and had a bonus of being faster. The other characters were okay to lose, although it was sometimes fun to play them.

Melee also had a faster speed than Brawl. :P

Roy is outdated. The Smash trend is that they take the classic game's hero, Marth, and the newest. Roy's game was near the end of development when Melee was in development, so they used Marth and Roy. The most recent games at Brawl's time both involved Ike, so naturally they used him. Roy is basically nothing to the series, to be honest. :/

Well, In Fire Emblem GBA Eliwood, Lyndis, and Hector were featured in that. But they are in Binding Blade which gives them two games. Now the point I'm trying to make here is if they were in Melee I bet they would be in brawl. But before that every game was a new refreshing plot with different characters in each one. But Ike was first to star in 2 of them, giving him an upper advantage over Roy. (Especially since Ike's games were sold out of Japan) Also making him much more well known around the world and making him a better choice for brawl. Who knows though. Maybe besides remakes they will continue with Ike being featured. If they did that then they'd never take him out.