This whole thread is based on OPs willful evasion of the difference between Palestinians living in the West Bank and Gaza, and Israeli nationals of Arab ethnicity.
Palestinians living in the occupied territories aren't second class Israeli citizens. They're not Israeli citizens at all. They're an enemy population, being indoctrinated into hating Israel and killing Jews from childhood until they die, by a government that is at war with Israel. Of course Israel discriminates against them. Every nation state discriminates against foreign nationals, as they should. The expectation that Israel, or the US, or any other state treat foreigners the same way it treats its own citizens, is unreasonable. Especially in the middle of a war. Calling that act of self defense apartheid is just childish name calling, by people who are at a loss of actual arguments.
Meanwhile, there is another group of Arabs, who are Israeli citizens. None of the laws and cases OP cites are discriminatory against Israelis of Arab ethnicity. Ethnic Arabs in Israel have the same exact rights Jews do, and, as Leonid said, one fewer obligations.