The difference here is that Everton has posted their losses so it is easy for the prem to look at it and say that it is over the 105m limit over 3 years and there isn’t really any debate about that. With City and Chelsea they have to prove that the money recorded in their income came from disallowed sources and that is a much harder case which involves a lot of lawyers and time. So it’s not really a case of Everton being poor so much as Everton has admitted to breaking the rule while City is denying it and I’d assume Chelsea is as well but I haven’t really read much about their situation yet.
I think the most obvious answer to this is Suarez, that last season was in my opinion the most dominant performance by any player in a single premier league season. If that Liverpool team had been as good as the current Liverpool or Man City sides I have no doubt that he would have scored close to 40 even without penalties.