If that was actually an issue, The Pokemon Trainer would have Piplup, Grotle, and Infernape instead of Squirtle, Ivysaur, and Charizard.
Um... no, and I'll show you why:
First Gen game covers: Venusaur (evolution of Ivysaur), Blastoise (evolution of Squirtle), Charizard, Pikachu.
Secondd Gen game covers: Ho-oh, Lugia, Suicune.
Third Gen game covers: Groundon, Kyogre, Raquaza
Fourth Gen game covers: Dialga and Palkia
Excluding first gen, the games moved away from even caring about the starters. Only Gen-1 has starters that anyone cares about really. Its what makes all the talk of Rival and other Pokemon Trainers being playable so stupid. Red is the Pokemon trainer we all remember, whatever we named him doesn't matter, Red-hatted kid is who we know.
Mario, Luigi, Peach, Bowser, and Wario. YES HE COUNTS.
Link, Zelda, Sheik, Toon Link, and Ganondorf.
Hell, the Pokemon Trainer pretty much counts as three by himself.
Yes, but, Wario and Yoshi (who you forgot) are not listed with the Mario emblem, Mario victory, or Mario stages. Zelda series and Pokemon series only have four characters on the select screen, which is what they were limiting. It'd be odd if we have these perfect series rows and then Mewtwo dog legging off the Pokemon set.
Roy got knocked aside by Ike, who essentially has the same moveset, only in the body of a better-known character; and Mewtwo got knocked aside by Lucario, a cooler and currently more popular Pokemon. That's all there is to it.
If you think Roy and Ike could EVER have the same moveset (except in some weird Mother series way) you don't know jack about the Fire Emblem series. Ike shares at most two moves with Roy and Marth (and that's only if you take a very liberal way of evaluating moves), and there isn't any connection from Ike's side and up specials to put them in the same ballpark as Roy's moveset. Ike's moveset has about as much in common with Roy's as Bowser does with Yoshi.
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Roy-kun: At the comment about the FE4 swords being better than the Sword of Seals. Sword of Seals is the only sword I know of in the series with an arbitrary and uneeded healing factor attached to it. Which, given it already has more than equalizing stats, abilities, and range given that this was before Magic ranged swords became more standardized... it just was way too useful in compare to any other FE weapon.