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Regarding the tier list in Skullgirls, Mike Z (the Lead Designer) has said that the tier list changes dramatically depending on who you talk to. "There are some people who think Parasoul is the best character in the game, and other people who can't stand her. Some groups swear by Painwheel, while others think she's useless." It all depends on who's holding the controller.
That being said, I don't think there really can be a solid, universal tier list in this game. Personally, I'd compare it to types in Pokémon, where certain characters and teams have advantages and disadvantages against other characters/teams.
1.) Pokemon has a tier list. That's what Uber/OU/UU is. Some pokemon are so strong, no matter who you use to try and gain an advantage over them, that they are detrimental to the entertainment value of the metagame, and as such are banned from standard play and put in ubers.
2.) Who is holding the controller does not change what characters are objectively better. You can argue that people don't currently know who is objectively better, but if you're honestly trying to state that the game is perfectly balanced, and that no character is objectively better than another character, you're ridiculous.
3.) Nobody good at Marvel says Viper is ~top 3, or even Top 5, in general. Theoryfighters that don't take human limitations into account call her top tier, but they're never good at marvel and never deal with the reality of top level competition. This isn't from your quote, but some clownshoe tried to use it to justify Marvel tiers being flawed, which is silly. Ultimate Marvel has been out for a couple years, and relatively clear tier lists.
When I brought up Pokémon, I was referring to types, not individual Pokémon. That is, there isn't a single best or worst type to use, because they all have advantages/disadvantages against each other. Steel might be an awesome type defensively, but Fire types have an edge against them. This still doesn't promise victory, but it helps. Once you consider stats and abilities and moves, that kinda mucks it up a little bit. I should've been more specific there.
I wouldn't say that Skullgirls is perfectly balanced, as evidenced by the fact that Mike Z insists on making subtle changes and improvements all the time. I would like to think that any one character being objectively better than another would only be better by a small margin.