So I finished this.
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If each of these companies got a second character for parity (I don't necessary think they should, mind you) I would prefer it to be these choices.
Tails because Sonic and Tails is an iconic duo, possibly close to the level of the Mario Bros, and because Sega doesn't have any
really noteworthy characters for Smash besides Sonic characters.
Lloyd because
he's perfect he could be a rival to Cloud in a way, the most well-known but not recurring protagonist from a single game in a long-running JRPG series. Also because the Symphonia games are both on the GameCube.
Lara Croft because she's an iconic character and because, if Sakurai decided to budge on the idea, a character that dual wields pistols would be extremely unique.
Simon Belmont because it's history is like 80% Nintendo; he, along with Mega Man is probably the most "Nintendo" non-Nintendo character you could add.
Disclaimer: This is just for fun. I'd like all of these choices but I don't want any to be added solely for parity.