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Wintropy
While an interesting idea... it just wouldn't be fair to the character. And I say this because of one other character - Dr. Mario. The Doc could've easily been an alt, but was made a fighter, even bringing back his taunt, some victory poses, and even the exact same moveset from SSBM. Relegating Roy to an alternate costume slot just wouldn't cut it; the addition of Doc as his own playable entity clearly shows Sakurai remembers and respects veterans of the past, clones and all.
Sakurai's mentioned how characters "that differ enough" from whom they're intended to be an alt costume of get their own slot. In this case, Roy is known for his fire prowess. Marth (or in your example, Chrom) lacks this quality. Just as Doc throwing pills and lacking FLUDD, or Dark Pit using his staff for his FS and Electroshock for his side special, warranted those characters a slot, Roy utilizing a fire element on his sword would be enough to keep him from being an alt of Marth or the like. That, and he still has a pretty faithful and somewhat vocal fanbase.
Sakurai's mentioned how characters "that differ enough" from whom they're intended to be an alt costume of get their own slot. In this case, Roy is known for his fire prowess. Marth (or in your example, Chrom) lacks this quality. Just as Doc throwing pills and lacking FLUDD, or Dark Pit using his staff for his FS and Electroshock for his side special, warranted those characters a slot, Roy utilizing a fire element on his sword would be enough to keep him from being an alt of Marth or the like. That, and he still has a pretty faithful and somewhat vocal fanbase.