I think that it's something of an illusion that Kassadin can be countered simply by building MR-- for indeed any AP carry can be made less effective by itemizing for magic resistance, but at what cost? If you sink 1K into MR, then you've essentially used 10% of your available resources to survive a single champion, but you've done nothing to enable yourself to kill them or stop the rest of their team. In the particular case of Kassadin, this isn't even true itself since so much of his strength comes from the fact that he can lay down a gank on bottom, and then immediately relocate back up to top and be ready to teamfight (since you've been managing your ult stacks)--something that no other champion can do.
Utilizing the criteria which you have set forth has a fundamental problem: is Graves is "low-tier" because he has exclusively AD damage, which is "countered" by armour (a myth, as addressed above, especially due to the prevalence of penetration items), then do you suggest not having any AD, simply because AD can be countered by armour? Clearly, that is a fallacy and an illogical premise to begin with.
The problem with League/MOBAs, as opposed to fighting games, is that you need to look at things in the aggregate. It is not about specific champions, but rather compositions as a whole. Gragas and Janna do not synergize well, yet they are both incredibly strong champions in their own right.