It is clear from the Gemorah and Meforshim Rishonim and Achronim that the type of punishment indicates what’s worse.
You are somewhat correct (Ayin BB 88B for a large exception), but that is not relevant to the point being made. Someone who doesn’t know (or recognize) that Chillul Shabbos is a problem (e.g. a Tinok Shenishba) will be punished less for that than someone who is MeAnes, or someone who cheats, while knowing it is wrong. Only the Ribbono Shel Olam knows what a person’s situation is and what they should be doing B’Asher Hu Sham.
Secondly, GAW, if a frei Yid knows that the Torah is true (even without internalizing it) and does not keep it, he is a rosha.
Judge not, that ye be not judged.
(In general, it’s not a bad idea, and certainly to those who have taken a step up so they should not look poorly on everyone below tham)
Once again, you don’t know where someone is holding and what the Ribbono Shel Olam expects from them in their situation to declare them to be a “Rasha”*. Perhaps they passed (or are passing) their Nisayon, and are doing what Hashem requires from them.
* There are exceptions, such as hitting someone or cheating, for which Chazal or the Torah (resp.) call someone who does them a “Rasha”.