If you listen to LCS long enough, you'll hear how someone bought a QSS as paying the Skarner tax (or the Malz text, etc). The idea is that these champions have such a strong ult, you need an item to counter it... and by countering it, you make the champion useless.
Think back to the (ridiculous, imo) justification for changing invisibility. Champs like Vayne and Akali have invisibility as part of their kit, and having an item completely negate that was seen as unfair. Now there is no counter to those abilities.
The question, then, is why the discrepancy? Why are game-changing ults allowed to be countered by an item, whereas Akali's cloud or Vayne's tumble is not? True, a QSS is a (full?) item whereas a ward is a ward, but both require gold and item slots, and both are built to completely nullify another champ's abilities. Why is invisibility special?
I'm not arguing that one or the other needs to be buffed or nerfed (though seriously, an 8sec uncounterable invisibility cloud at lvl2? Come on rito), but I am arguing that there is a disconnect here. Should items be allowed to hard counter champion abilities or not? If yes, then invisibility should have a counter. If no, then the game-changing ults and abilities should not be countered. Other balance changes would certainly need to happen as well, but there should be a consistent philosophy when it comes to items.