Dark Samus is there and she didn't exist until after the Gamecube, so I didn't make that a rule.
Ah, gotcha. So whatever goes. Thanks for clearing it up.
(To clarify, I get how the Mod works, but I wanted to make sure I understood what PeridotGX's rules were instead. Not simply the mod itself).
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Anyway, onto it;
Dr. Mario. While I do like Wario, I feel using him as a different kind of clone is neat. One that could be a heavier Mario. Luigi is more like the lighter one. It could be seen somewhat as a Mario Kart-like dynamic.
Brian. I mean, obviously you know I want him in, but I've noticed he makes for a great body shape too, and a lot of similar potential abilities to remake him. Of course, you'd need to do some very unique changes. Like, Brian can't do PK Fire very well, but you could do a similar mechanic but using Charizard's Flamethrower somewhat(the pokeball) to capture it. PK Thunder is actually pretty similar in essence to Homing Arrow too. And PSI Shield actually has similarities to Confusion as is(which is absorbing damage into MP. But just having it work like PSI Shield is fine too, as it'd combine Confusion and Healing).
Wolf. I like antagonists, and I feel he could make for an interesting change. Being more heavy-based as is.
Dark Link, somewhat akin to how Ganondorf is done, based around darkness. They could also focus on more Zelda II abilities instead, not just the Up and Downthrusts. For instance, his Final Smash could be Thunder, weakening everyone's defenses and doing a good amount of damage.
Like others, I think Pichu is a great fit! I feel like Ultimate made him a bit OP, missing the point of its Joke Character status.
Boshi. Now, obviously this is kind of silly if Geno isn't in, but Geno really has no one to go off of until 4 with MegaMan getting close(same with Mii Gunner). Samus has the gun part, but a completely off build. Admittedly you could use Ness too? Anyway, Boshi already had potential similar skills to Yoshi, but stuff like Cookies being used along with SMRPG items could be taken into account. In addition to that, you have various moves from enemies like Croco, so having a Bomb Egg for an Up B would change it up but still capture the nastiness that Boshi is.
Some other thoughts are Ganondorf, Dark Samus, Black Shadow, Wario, and Funky Kong. Wario is one I feel can't be captured too well as being a clone anyway. It doesn't do him justice. Smash doesn't focus on my favorite style of Wario, but it still captures how he's vastly different from Mario while keeping with his actual games regardless. I mean, giving the option, I'd gladly remove the Wario Waft for his Ground Pound or another Land move where possible otherwise, but I do like him a lot more than I used to.