Just because the Mario series did something, doesn't mean everything should follow suit. The reason it is like that is because:
-Luigi was established as a character in Mario Bros.
-Peach and Bowser were established in Super Mario Bros.
-Yoshi got his own game, meriting his inclusion its own series.
If that logic applies to Sonic, that means Eggman comes first, follows by Tails, Amy and Metal, Knuckles, and lastly Shadow.
There's another consideration here, too. Tails can be more easily cloned than Eggman.
Also, villains seem to have lower priority in general than heroes when it comes to Smash. It's not just Mario that puts the sidekick or a secondary hero in there before a villain who appeared sooner. Look at Earthbound. We get Lucas instead of Porky. Look at Fire Emblem. We get Roy and Ike instead of whoever the villain from the first game there is. Look at Metroid. We get Zero Suit Samus instead of Ridley.
Seniority of a character is very important, but it's not the end-all-be-all, else we'd have Pauline be playable. Neither is a character's popularity, otherwise Geno would be playable. Neither is a character's cloneability, else we'd have Dark Samus be playable. You can't just look at one aspect of a set of characters and choose from that. You have to take
everything into account. I'm not saying Eggman's a bad choice. He'd work. But Tails would work better.
Which by that logic means Shadow > Tails. Your point? Just because a Sonic character is added doesn't mean it has to be a clone of Sonic himself.
No, it doesn't. Shadow and Tails would be equally cloneable, but Tails has seniority. Yes, Eggman has more seniority than even that, but Tails is cloneable.
Eggman = Senior character
Shadow = Cloneable
Tails = Senior character AND Cloneable